Convergent evolution of processivity in bacterial and fungal cellulases.

Cellulose is the most abundant biomass on Earth, and many microorganisms depend on it as a source of energy. It consists mainly of crystalline and amorphous regions, and natural degradation of the crystalline part is highly dependent on the degree of processivity of the degrading enzymes (i.e., the extent of continuous hydrolysis without detachment from the substrate cellulose). Here, we report high-speed atomic force microscopic (HS-AFM) observations of the movement of four types of cellulases derived from the cellulolytic bacteria Cellulomonas fimi on various insoluble cellulose substrates. The HS-AFM images clearly demonstrated that two of them (CfCel6B and CfCel48A) slide on crystalline cellulose. The direction of processive movement of CfCel6B is from the nonreducing to the reducing end of the substrate, which is opposite that of processive cellulase Cel7A of the fungus Trichoderma reesei (TrCel7A), whose movement was first observed by this technique, while CfCel48A moves in the same direction as TrCel7A. When CfCel6B and TrCel7A were mixed on the same substrate, "traffic accidents" were observed, in which the two cellulases blocked each other's progress. The processivity of CfCel6B was similar to those of fungal family 7 cellulases but considerably higher than those of fungal family 6 cellulases. The results indicate that bacteria utilize family 6 cellulases as high-processivity enzymes for efficient degradation of crystalline cellulose, whereas family 7 enzymes have the same function in fungi. This is consistent with the idea of convergent evolution of processive cellulases in fungi and bacteria to achieve similar functionality using different protein foldings.

Domain architecture divergence leads to functional divergence in binding and catalytic domains of bacterial and fungal cellobiohydrolases.

Cellobiohydrolases directly convert crystalline cellulose into cellobiose and are of biotechnological interest to achieve efficient biomass utilization. As a result, much research in the field has focused on identifying cellobiohydrolases that are very fast. Cellobiohydrolase A from the bacterium Cellulomonas fimi (CfCel6B) and cellobiohydrolase II from the fungus Trichoderma reesei (TrCel6A) have similar catalytic domains (CDs) and show similar hydrolytic activity. However, TrCel6A and CfCel6B have different cellulose-binding domains (CBDs) and linkers: TrCel6A has a glycosylated peptide linker, whereas CfCel6B's linker consists of three fibronectin type 3 domains. We previously found that TrCel6A's linker plays an important role in increasing the binding rate constant to crystalline cellulose. However, it was not clear whether CfCel6B's linker has similar function. Here we analyze kinetic parameters of CfCel6B using single-molecule fluorescence imaging to compare CfCel6B and TrCel6A. We find that CBD is important for initial binding of CfCel6B, but the contribution of the linker to the binding rate constant or to the dissociation rate constant is minor. The crystal structure of the CfCel6B CD showed longer loops at the entrance and exit of the substrate-binding tunnel compared with TrCel6A CD, which results in higher processivity. Furthermore, CfCel6B CD showed not only fast surface diffusion but also slow processive movement, which is not observed in TrCel6A CD. Combined with the results of a phylogenetic tree analysis, we propose that bacterial cellobiohydrolases are designed to degrade crystalline cellulose using high-affinity CBD and high-processivity CD.

Nodular Pseudogout of the Skull Base Arising From the Temporomandibular Joint.

ABSTRACT: The authors report a case of a rare, large, nodular pseudogout which developed from the temporomandibular joint (TMJ).An 83-year-old female was referred to the hospital with swelling on her left cheek. Imaging studies revealed a large calcified mass surrounding the left mandibular condyle, partially destroying the adjoining bone and extending to the skull base. Magnetic resonance imaging (MRI) revealed soft tissue masses with low signal intensity on T1- and T2-weighted images and were enhanced after intravenous gadolinium injection.The mass was clinically and radiologically suspected to be a neoplastic lesion, such as chondrosarcoma or fibrous dysplasia. However, histological analysis showed that the mass contained granulomatous lesions with numerous multiple nodular rod-shaped and diamond-shaped crystal deposits, which validated the diagnosis of pseudogout. X-ray diffraction (XRD) was performed to identify the tumor's deposited materials and revealed that these were calcium pyrophosphate dihydrate (CPPD) crystals. This result confirmed the histopathological diagnosis of "tophaceous pseudogout."

Single-molecule Imaging Analysis of Binding, Processive Movement, and Dissociation of Cellobiohydrolase Trichoderma reesei Cel6A and Its Domains on Crystalline Cellulose.

Trichoderma reesei Cel6A (TrCel6A) is a cellobiohydrolase that hydrolyzes crystalline cellulose into cellobiose. Here we directly observed the reaction cycle (binding, surface movement, and dissociation) of single-molecule intact TrCel6A, isolated catalytic domain (CD), cellulose-binding module (CBM), and CBM and linker (CBM-linker) on crystalline cellulose Iα The CBM-linker showed a binding rate constant almost half that of intact TrCel6A, whereas those of the CD and CBM were only one-tenth of intact TrCel6A. These results indicate that the glycosylated linker region largely contributes to initial binding on crystalline cellulose. After binding, all samples showed slow and fast dissociations, likely caused by the two different bound states due to the heterogeneity of cellulose surface. The CBM showed much higher specificity to the high affinity site than to the low affinity site, whereas the CD did not, suggesting that the CBM leads the CD to the hydrophobic surface of crystalline cellulose. On the cellulose surface, intact molecules showed slow processive movements (8.8 ± 5.5 nm/s) and fast diffusional movements (30-40 nm/s), whereas the CBM-Linker, CD, and a catalytically inactive full-length mutant showed only fast diffusional movements. These results suggest that both direct binding and surface diffusion contribute to searching of the hydrolysable point of cellulose chains. The duration time constant for the processive movement was 7.7 s, and processivity was estimated as 68 ± 42. Our results reveal the role of each domain in the elementary steps of the reaction cycle and provide the first direct evidence of the processive movement of TrCel6A on crystalline cellulose.

[A Case of Aplastic or Twig-Like Middle Cerebral Artery Presenting with an Intracranial Hemorrhage Two Years after a Transient Ischemic Attack].

Aplastic or twig-like middle cerebral artery (Ap/T-MCA) is a rare anatomical anomaly, which can be associated with intracranial hemorrhage and cerebral ischemia. A 52-year-old woman who presented with sudden headache was admitted to our hospital. Computed tomography (CT) and magnetic resonance imaging showed no abnormality; however, magnetic resonance angiogram revealed an occlusion or severe stenosis in the left middle cerebral artery. Three-dimensional CT angiography demonstrated severe stenosis in the left middle cerebral artery. The patient was discharged without any neurological deficit; however, she subsequently complained of temporary weakness in the right hand. It was possibly due to a transient ischemic attack; therefore, cilostazol 200 mg/day was administered for prevention of cerebral ischemia. Single photon emission computed tomography(with or without administration of acetazolamide)showed neither significant decrease in the cerebral blood flow nor cerebrovascular reactivity; hence, surgical revascularization was not performed. However, two years after the initial admission, she was urgently admitted to our hospital with sudden headache and nausea followed by aphasia and weakness of the right extremities. CT images showed diffuse subarachnoid hemorrhage and intracerebral hemorrhage in the left temporo-parietal lobe. Cerebral angiography revealed that the left middle cerebral artery was Ap/T-MCA without cerebral aneurysms. The patient was treated conservatively, and she eventually recovered without any neurological deficit except mild aphasia. Since Ap/T-MCA is associated with both hemorrhagic and ischemic stroke, antiplatelet therapy should be administered carefully. Moreover, it is necessary to consider extracranial-intracranial bypass to reduce hemodynamic stress on the abnormal vessels.

Characterization of a novel ß-glucosidase from a compost microbial metagenome with strong transglycosylation activity.

The ß-glucosidase encoded by the td2f2 gene was isolated from a compost microbial metagenomic library by functional screening. The protein was identified to be a member of the glycoside hydrolase family 1 and was overexpressed in Escherichia coli, purified, and biochemically characterized. The recombinant ß-glucosidase, Td2F2, exhibited enzymatic activity with ß-glycosidic substrates, with preferences for glucose, fucose, and galactose. Hydrolysis occurred at the nonreducing end and in an exo manner. The order of catalytic efficiency for glucodisaccharides and cellooligosaccharides was sophorose > cellotetraose > cellotriose > laminaribiose > cellobiose > cellopentaose > gentiobiose, respectively. Intriguingly, the p-nitrophenyl-ß-D-glucopyranoside hydrolysis activity of Td2F2 was activated by various monosaccharides and sugar alcohols. At a D-glucose concentration of 1000 mM, enzyme activity was 6.7-fold higher than that observed in the absence of D-glucose. With 31.3 mM D-glucose, Td2F2 catalyzed transglycosylation to generate sophorose, laminaribiose, cellobiose, and gentiobiose. Transglycosylation products were detected under all activated conditions, suggesting that the activity enhancement induced by monosaccharides and sugar alcohols may be due to the transglycosylation activity of the enzyme. These results show that Td2F2 obtained from a compost microbial metagenome may be a potent candidate for industrial applications.

Ultrasonography monitoring with Superb Microvascular Imaging during cerebrovascular surgery.

INTRODUCTION: Ultrasonography (US) is used as a real-time dynamic imaging modality during neurosurgery. A novel Doppler US technique, Superb Microvascular Imaging (SMI), can be used to visualize low-velocity flow of small vessels at high resolution with high frame rates. We visualized vessel flow using this US SMI technique and contrast agent during cerebrovascular surgery. METHODS: Forty-three patients with an unruptured cerebral aneurysm (control), ischemic and hemorrhagic moyamoya disease, carotid artery stenosis, hemangioblastoma, severe stenosis of the middle cerebral artery, venous angioma, and intracerebral hemorrhage (ICH) underwent neurosurgery with US SMI monitoring using a contrast agent. The diameter, length, and number of penetrating vessels were analyzed in patients with an unruptured cerebral aneurysm (control), moyamoya disease, and ICH. RESULTS: Diameter and length of cerebral penetrating vessels were significantly increased in patients with moyamoya disease and ICH compared to control patients. The number of penetrating vessels was increased in moyamoya disease patients compared to control and ICH patients. In hemorrhagic moyamoya disease, flow in the penetrating vessels originated from a deep periventricular point and extended to the cerebral surface. Pulsatile cerebral aneurysms during clipping surgery and carotid artery stenosis during carotid endarterectomy were easily identified by SMI. Drastically increased vessel flow in patients with a hemangioblastoma or a venous angioma was observed. CONCLUSION: Using the US SMI technique and contrast agent, we obtained useful flow information of the vascular disease structure and intracerebral deep small vessels during cerebrovascular surgery. Further quantitative analysis will be informative and helpful for cerebrovascular surgery.

[A case of cerebellar variant of posterior reversible encephalopathy syndrome in puerperium].

A 29-year-old woman complained of headache and nausea several hours after delivery, followed by mild disturbance of consciousness. Physical examination revealed hypertension, systemic edema, nystagmus, dysarthria, and cerebellar ataxia. Computed tomography showed low attenuation areas in the cerebellum, and MR imaging revealed vasogenic edema in the cerebellum. MR angiography and MR venography demonstrated no significant abnormalities. We diagnosed a cerebellar variant of posterior reversible encephalopathy syndrome(PRES), and treated the patient immediately with antihypertensive drug and diuretic. The symptoms dramatically improved and MR imaging ten days after admission revealed disappearance of the vasogenic edema in the cerebellum. She was discharged without any sequelae. Though a cerebellar variant of PRES is very rare, rapid diagnosis and treatment is important for good prognosis when the disease is encountered.

[Blood blister-like aneurysm on the posterior wall of the internal carotid artery causing subarachnoid hemorrhage: a case report].

We report a case of blood blister-like aneurysm(BBA)on the posterior wall of the internal carotid artery(ICA)causing subarachnoid hemorrhage(SAH). A 45-year-old man suffering from SAH(WFNS grade 5)was referred to our hospital. 3D-CT angiography showed a BBA on the posterior wall of the ICA. The aneurysm had been enlarged for a few days. Therefore we performed coil embolization. Four weeks after the operation, the aneurysm was found to have regrown. In the second operation the aneurysm was successfully treated by the ICA proximal occlusion with extracranial-intracranial bypass. Postoperative follow-up cerebral angiography detected no aneurysm. To our knowledge, BBA on the posterior wall of the ICA is rare. Radical surgery with bypass should be performed as soon as possible when the BBA is found to regrow. We discuss the clinical characteristics with a review of the literature.

[A case of cervicothoracic subpial lipoma].

We report the case of a 24-year-old woman with cervicothoracic subpial lipoma not associated with spinal dysraphism. She complained of back pain, gait disturbance, and sensory disturbance of the both lower extremities. MRI revealed a hyperintense mass lesion that was dorsolateral to the spinal cord in the intradural region between C7 and Th4 on both T1 and T2 weighted images. Axial T2 weighted images showed dorsal nerve roots passing through the mass. A thoracic laminectomy between Th1 and Th4 was performed. A yellowish subpial mass was found after the dura was opened, and the borderline between the tumor and the normal spinal cord was unclear. The mass was partially resected and intraoperative SEP monitoring data remained unchanged. Dural plasty using artificial dura was performed. Histological examination revealed mature adipose and connective tissues, a fact which was compatible with a diagnosis of lipoma. Postoperatively, no complications occurred. The patient's gait disturbance and hypesthesia of the right lower extremity slightly improved. Subpial spinal lipoma not associated with dysraphism is rare and accounts for only 1% of all spinal tumors. A slow ascending spastic monoparesis or paraparesis is a common initial symptom. However, once symptoms progress, further deterioration is rapid. Therefore, early surgical decompression and debulking of the subpial lipoma in patients with neurological abnormalities is recommended because most symptomatic patients do not improve after surgery.

Lytic polysaccharide monooxygenase increases cellobiohydrolases activity by promoting decrystallization of cellulose surface.

Efficient depolymerization of crystalline cellulose requires cooperation between multiple cellulolytic enzymes. Through biochemical approaches, molecular dynamics (MD) simulation, and single-molecule observations using high-speed atomic force microscopy (HS-AFM), we quantify and track synergistic activity for cellobiohydrolases (CBHs) with a lytic polysaccharide monooxygenase (LPMO) from Phanerochaete chrysosporium. Increasing concentrations of LPMO (AA9D) increased the activity of a glycoside hydrolase family 6 CBH, Cel6A, whereas the activity of a family 7 CBH (Cel7D) was enhanced only at lower concentrations of AA9D. MD simulation suggests that the result of AA9D action to produce chain breaks in crystalline cellulose can oxidatively disturb the crystalline surface by disrupting hydrogen bonds. HS-AFM observations showed that AA9D increased the number of Cel7D molecules moving on the substrate surface and increased the processivity of Cel7D, thereby increasing the depolymerization performance, suggesting that AA9D not only generates chain ends but also amorphizes the crystalline surface, thereby increasing the activity of CBHs.

A case of a rosette-forming glioneuronal tumor with clinicopathological features of a dysembryoplastic neuroepithelial tumor and fibroblast growth factor receptor 1 internal tandem duplication.

Rosette-forming glioneuronal tumors (RGNTs) are benign WHO grade 1 tumors that occur in the ventricular system, particularly the fourth ventricle. RGNTs and dysembryoplastic neuroepithelial tumors (DNTs) are both categorized as neuronal and mixed neuronal-glial tumors and may be difficult to distinguish. Coexistence of the two tumor types has been reported. Here, we report a pediatric case of RGNT with DNT-like features showing intraventricular dissemination. The tumor occurred in the medial temporal lobe and presented with specific pathological glioneuronal elements including floating neurons, which are typical in DNTs, but was diagnosed as RGNT because of the presence of neurocytic rosettes. Genetic analysis detected fibroblast growth factor receptor 1 internal tandem duplication (FGFR1-ITD) of the tyrosine kinase domain, which was previously reported to be specific for DNT. RGNTs with FGFR1-ITD may show atypical clinical presentation and pathological features.

Product-induced gene expression, a product-responsive reporter assay used to screen metagenomic libraries for enzyme-encoding genes.

A reporter assay-based screening method for enzymes, which we named product-induced gene expression (PIGEX), was developed and used to screen a metagenomic library for amidases. A benzoate-responsive transcriptional activator, BenR, was placed upstream of the gene encoding green fluorescent protein and used as a sensor. Escherichia coli sensor cells carrying the benR-gfp gene cassette fluoresced in response to benzoate concentrations as low as 10 µM but were completely unresponsive to the substrate benzamide. An E. coli metagenomic library consisting of 96,000 clones was grown in 96-well format in LB medium containing benzamide. The library cells were then cocultivated with sensor cells. Eleven amidase genes were recovered from 143 fluorescent wells; eight of these genes were homologous to known bacterial amidase genes while three were novel genes. In addition to their activity toward benzamide, the enzymes were active toward various substrates, including d- and l-amino acid amides, and displayed enantioselectivity. Thus, we demonstrated that PIGEX is an effective approach for screening novel enzymes based on product detection.

Iron-corroding methanogen isolated from a crude-oil storage tank.

Microbiologically influenced corrosion of steel in anaerobic environments has been attributed to hydrogenotrophic microorganisms. A sludge sample collected from the bottom plate of a crude-oil storage tank was used to inoculate a medium containing iron (Fe(0)) granules, which was then incubated anaerobically at 37 degrees C under an N(2)-CO(2) atmosphere to enrich for microorganisms capable of using iron as the sole source of electrons. A methanogen, designated strain KA1, was isolated from the enrichment culture. An analysis of its 16S rRNA gene sequence revealed that strain KA1 is a Methanococcus maripaludis strain. Strain KA1 produced methane and oxidized iron much faster than did the type strain of M. maripaludis, strain JJ(T), which produced methane at a rate expected from the abiotic H(2) production rate from iron. Scanning electron micrographs of iron coupons that had been immersed in either a KA1 culture, a JJ(T) culture, or an aseptic medium showed that only coupons from the KA1 culture had corroded substantially, and these were covered with crystalline deposits that consisted mainly of FeCO(3).

Timelined multimodal recording of EEG and driving performance using a driving simulator system during a focal impaired awareness seizure.

An epileptic seizure during the course of driving can result in a serious car accident. However, basic data on how epileptic seizures actually affect driving performance is significantly lacking. To understand the relationship, it is crucial to conduct not only behavioral but also electroencephalogram (EEG) analysis during epileptic seizures. Therefore, we developed a mobile driving simulator which makes it possible to record driving-related parameters time-lined with video-EEG. We report a case in which behavioral and EEG changes were successfully recorded during ictal periods of focal impaired awareness seizure in a patient engaged with the system. With the current lack of objective data describing how seizures impair driving performance, such an accumulation of information could improve personalized medical management, influence legal adjudication and assist in the development of driving support systems for people with epilepsy.

Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes.

Recent awareness that most microorganisms in the environment are resistant to cultivation has prompted scientists to directly clone useful genes from environmental metagenomes. Two screening methods are currently available for the metagenome approach, namely, nucleotide sequence-based screening and enzyme activity-based screening. Here we have introduced and optimized a third option for the isolation of novel catabolic operons, that is, substrate-induced gene expression screening (SIGEX). This method is based on the knowledge that catabolic-gene expression is generally induced by relevant substrates and, in many cases, controlled by regulatory elements situated proximate to catabolic genes. For SIGEX to be high throughput, we constructed an operon-trap gfp-expression vector available for shotgun cloning that allows for the selection of positive clones in liquid cultures by fluorescence-activated cell sorting. The utility of SIGEX was demonstrated by the cloning of aromatic hydrocarbon-induced genes from a groundwater metagenome library and subsequent genome-informatics analysis.

An extracellular [NiFe] hydrogenase mediating iron corrosion is encoded in a genetically unstable genomic island in Methanococcus maripaludis.

Certain methanogens deteriorate steel surfaces through a process called microbiologically influenced corrosion (MIC). However, the mechanisms of MIC, whereby methanogens oxidize zerovalent iron (Fe0), are largely unknown. In this study, Fe0-corroding Methanococcus maripaludis strain OS7 and its derivative (strain OS7mut1) defective in Fe0-corroding activity were isolated. Genomic analysis of these strains demonstrated that the strain OS7mut1 contained a 12-kb chromosomal deletion. The deleted region, termed "MIC island", encoded the genes for the large and small subunits of a [NiFe] hydrogenase, the TatA/TatC genes necessary for the secretion of the [NiFe] hydrogenase, and a gene for the hydrogenase maturation protease. Thus, the [NiFe] hydrogenase may be secreted outside the cytoplasmic membrane, where the [NiFe] hydrogenase can make direct contact with Fe0, and oxidize it, generating hydrogen gas: Fe0 + 2 H+ → Fe2+ + H2. Comparative analysis of extracellular and intracellular proteomes of strain OS7 supported this hypothesis. The identification of the MIC genes enables the development of molecular tools to monitor epidemiology, and to perform surveillance and risk assessment of MIC-inducing M. maripaludis.

Improved inverse PCR scheme for metagenome walking.

Inverse PCR has been used for the recovery of genome regions flanking a known sequence, although its application to metagenome walking is limited due to inefficient amplification from low copy number fragments. Here we present an improved inverse PCR scheme that enables walking of rare fragments in environmental metagenomes. Our scheme includes the following steps: (i) inverse PCR in which one primer is connected to an affinity tag; (ii) affinity purification of PCR products for removing background metagenome; and (iii) nested PCR to recover target flanking regions (IAN-PCR). In a model experiment, flanking regions of a gene fragment in Ralstonia eutropha were recovered from mixtures of Ralstonia and Escherichia genomes by standard inverse PCR, inverse PCR coupled to nested PCR (IN-PCR), and IAN-PCR, showing that they were recovered when ratios of Ralstonia genome to the background Escherichia genome were greater than 10(-1), 10(-3), and 10(-5), respectively. The utility of IAN-PCR was also examined by recovering flanking regions of PCR-amplified putative chitinase gene fragments from a groundwater metagenome, showing that IAN-PCR obtained flanking regions for more diverse gene fragments than IN-PCR. Since rare sequences are a critical element of natural genetic diversity, IAN-PCR enables access to undiscovered diverse genes in the environment.

Molecular directionality in crystalline beta-chitin: hydrolysis by chitinases A and B from Serratia marcescens 2170.

Beta-chitin microfibrils were treated with ChiA and ChiB (chitinases A and B respectively) from Serratia marcescens 2170. The beta-chitin microfibrils were shortened, and the tips appeared narrowed and sharpened at both ends, after either consecutive or simultaneous degradation by ChiA and ChiB. Increased production of reducing sugars by simultaneous degradation (by ChiA and ChiB) of beta-chitin, but not of glycol chitin, suggests synergistic interactions between the two enzymes. A combined analysis using the tilt microdiffraction method to determine the crystallographic axes, together with the biotin-streptavidin-gold-labelling method specific to the reducing ends, was used to investigate the polarity of the degraded beta-chitin microcrystals. The digestion of the beta-chitin fibrils by ChiA occurred from the reducing end to the nonreducing end, whereas digestion by ChiB occurred from the non-reducing end to the reducing end. The results are in agreement with the previously determined three-dimensional structures of these enzymes.

Development of simple random mutagenesis protocol for the protein expression system in Pichia pastoris.

BACKGROUND: Random mutagenesis is a powerful technique to obtain mutant proteins with different properties from the wild-type molecule. Error-prone PCR is often employed for random mutagenesis in bacterial protein expression systems, but has rarely been used in the methylotrophic yeast Pichia pastoris system, despite its significant advantages, mainly because large (µg-level) amounts of plasmids are required for transformation. RESULTS: We developed a quick and easy technique for random mutagenesis in P. pastoris by sequential Phi29 DNA polymerase-based amplification methods, error-prone rolling circle amplification (RCA) and multiple displacement amplification (MDA). The methodology was validated by applying it for random mutation of the gene encoding cellulase from the basidiomycete Phanerochaete chrysosporium (PcCel6A), a key enzyme in degradation of cellulosic biomass. In the error-prone RCA step, the concentrations of manganese ion (Mn(2+)) and cellulase gene-containing plasmid were varied, and the products obtained under each condition were subjected to the second MDA step in the absence of Mn(2+). The maximum error rate was 2.6 mutations/kb, as evaluated from the results of large-scale sequencing. Several µg of MDA products was transformed by electroporation into Pichia cells, and the activities of extracellularly expressed PcCel6A mutants towards crystalline and amorphous celluloses were compared with those of wild-type enzyme to identify key amino acid residues affecting degradation of crystalline cellulose. CONCLUSIONS: We present a rapid and convenient random mutagenesis method that does not require laborious steps such as ligation, cloning, and synthesis of specific primers. This method was successfully applied to the protein expression system in P. pastoris.