Super-enhancer trapping by the nuclear pore via intrinsically disordered regions of proteins in squamous cell carcinoma cells

Master transcription factors such as TP63 establish super-enhancers (SEs) to drive core transcriptional networks in cancer cells, yet the spatiotemporal regulation of SEs within the nucleus remains unknown. The nuclear pore complex (NPC) may tether SEs to the nuclear pore where RNA export rates are maximal. Here, we report that NUP153, a component of the NPC, anchors SEs to the NPC and enhances TP63 expression by maximizing mRNA export. This anchoring is mediated through protein-protein interaction between the intrinsically disordered regions (IDRs) of NUP153 and the coactivator BRD4. Silencing of NUP153 excludes SEs from the nuclear periphery, decreases TP63 expression, impairs cellular growth, and induces epidermal differentiation of squamous cell carcinoma. Overall, this work reveals the critical roles of NUP153 IDRs in the regulation of SE localization, thus providing insights into a new layer of gene regulation at the epigenomic and spatial level.

Structural Dynamics of E6AP E3 Ligase HECT Domain and Involvement of a Flexible Hinge Loop in the Ubiquitin Chain Synthesis Mechanism

Ubiquitin (Ub) ligases E3 are important factors in selecting target proteins for ubiquitination and determining the type of polyubiquitin chains on the target proteins. In the HECT (homologous to E6AP C-terminus)-type E3 ligases, the HECT domain is composed of an N-lobe and a C-lobe that are connected by a flexible hinge loop. The large conformational rearrangement of the HECT domain via the flexible hinge loop is essential for the HECT-type E3-mediated Ub transfer from E2 to a target protein. However, detailed insights into the structural dynamics of the HECT domain remain unclear. Here, we provide the first direct demonstration of the structural dynamics of the HECT domain using high-speed atomic force microscopy at the nanoscale. We also found that the flexibility of the hinge loop has a great impact not only on its structural dynamics but also on the formation mechanism of free Ub chains.

The SYP123-VAMP727 SNARE complex delivers secondary cell wall components for root hair shank hardening in Arabidopsis

The extended tubular shape of root hairs is established by tip growth and concomitant hardening. Here, we demonstrate that a syntaxin of plants (SYP)123-vesicle-associated membrane protein (VAMP)727-dependent secretion system delivers secondary cell wall components for hardening the subapical zone and shank of Arabidopsis (Arabidopsis thaliana) root hairs. We found increased SYP123 localization at the plasma membrane (PM) of the subapical and shank zones compared with the tip region in elongating root hairs. Inhibition of phosphatidylinositol (PtdIns)(3,5)P2 production impaired SYP123 localization at the PM and SYP123-mediated root hair shank hardening. Moreover, root hair elongation in the syp123 mutant was insensitive to a PtdIns(3,5)P2 synthesis inhibitor. SYP123 interacts with both VAMP721 and VAMP727. syp123 and vamp727 mutants exhibited reduced shank cell wall stiffness due to impaired secondary cell wall component deposition. Based on these results, we conclude that SYP123 is involved in VAMP721-mediated conventional secretion for root hair elongation as well as in VAMP727-mediated secretory functions for the delivery of secondary cell wall components to maintain root hair tubular morphology.

Elucidation of the Binding Mechanism of Anionic Phospholipids to Antioxidant Protein Peroxiredoxin 2

Peroxiredoxins (Prxs) belong to a family of ubiquitously expressed peroxidases that detoxify reactive oxygen species. In addition to their enzymatic function, Prxs also function as molecular chaperones. This functional switch is related to their degree of oligomerization. We have previously revealed that Prx2 interacts with anionic phospholipids and that the anionic phospholipid-containing Prx2 oligomer forms a high molecular weight (HMW) complex in a nucleotide-dependent manner. However, the detailed mechanism of the oligomer and HMW complex formation remains unclear. In this study, we investigated the anionic phospholipid binding site in Prx2 using site-directed mutagenesis to understand the mechanism of the oligomer formation. Our findings demonstrated that six binding site residues in Prx2 are important for the binding of anionic phospholipids.

Structural Dynamics of Amyloid-β Protofibrils and Actions of Anti-Amyloid-β Antibodies as Observed by High-Speed Atomic Force Microscopy

Amyloid-β (Aβ) aggregation intermediates, including oligomers and protofibrils (PFs), have attracted attention as neurotoxic aggregates in Alzheimer's disease. However, due to the complexity of the aggregation pathway, the structural dynamics of aggregation intermediates and how drugs act on them have not been clarified. Here we used high-speed atomic force microscopy to observe the structural dynamics of Aβ42 PF at the single-molecule level and the effect of lecanemab, an anti-Aβ PF antibody with the positive results from Phase 3 Clarity AD. PF was found to be a curved nodal structure with stable binding angle between individual nodes. PF was also a dynamic structure that associates with other PF molecules and undergoes intramolecular cleavage. Lecanemab remained stable in binding to PFs and to globular oligomers, inhibiting the formation of large aggregates. These results provide direct evidence for a mechanism by which antibody drugs interfere with the Aβ aggregation process.

Importance of annexin V N-terminus for 2D crystal formation and quick purification protocol of recombinant annexin V

Annexin V forms trimeric structures which further assemble into two-dimensional crystal (2D crystal) lattices on negatively charged phospholipid bilayer in a Ca2+-dependent manner. It is also known that annexin V 2D crystals show two types of symmetric patterns with six-fold symmetry (p6) and three-fold symmetry (p3). The p6 lattice also contains additional trimers in the gaps between the p6 axes, which are also referred to as non-p6 trimers because they do not participate in the formation of the p6 lattice. We here show that the annexin V N-terminal has significant influence on 2D crystal formation using high-speed atomic force microscopy (HS-AFM) observations. We also present a quick purification method to purify recombinant annexin V without any residual affinity tag after protein purification in ~3h.

Computational see-through screen camera based on a holographic waveguide device

This study proposes a novel computational imaging system that integrates a see-through screen (STS) with volume holographic optical elements (vHOEs) and a digital camera unit. Because of the unique features of the vHOE, the STS can function as a holographic waveguide device (HWD) and enable the camera to capture the frontal image when the user gazes at the screen. This system not only provides an innovative solution to a high-quality video communication system by realizing eye-contact but also contributes to other visual applications due to its refined structure. However, there is a dilemma in the proposed imaging system: for a wider field of view, a larger vHOE is necessary. If the size of the vHOE is larger, the light rays from the same object point are diffracted at different Bragg conditions and reflect a different number of times, which causes blurring of the captured image. The system imaging process is analyzed by ray tracing, and a digital image reconstruction method was employed to obtain a clear picture in this study. Optical experiments confirmed the effectiveness of the proposed HWD-STS camera.

Unraveling the Host-Selective Toxic Interaction of Cassiicolin with Lipid Membranes and Its Cytotoxicity

Cassiicolin (Cas), a toxin produced by Corynespora cassiicola, is responsible for Corynespora leaf fall disease in susceptible rubber trees. Currently, the molecular mechanisms of the cytotoxicity of Cas and its host selectivity have not been fully elucidated. Here, we analyzed the binding of Cas1 and Cas2 to membranes consisting of different plant lipids and their membrane disruption activities. Using high-speed atomic force microscopy and confocal microscopy, we reveal that the binding and disruption activities of Cas1 and Cas2 on lipid membranes are strongly dependent on the specific plant lipids. The negative phospholipids, glycerolipids, and sterols are more sensitive to membrane damage caused by Cas1 and Cas2 than neutral phospholipids and betaine lipids. Mature Cas1 and Cas2 play an essential role in causing membrane disruption. Cytotoxicity tests on rubber leaves of Rubber Research Institute of Vietnam (RRIV) 1, RRIV 4, and Prang Besar (PB) 255 clones suggest that the toxins cause necrosis of rubber leaves, except for the strong resistance of PB 255 against Cas2. Cryogenic scanning electron microscopy analyses of necrotic leaf tissues treated with Cas1 confirm that cytoplasmic membranes are vulnerable to the toxin. Thus, the host selectivity of Cas toxin is attained by the lipid-dependent binding activity of Cas to the membrane, and the cytotoxicity of Cas arises from its ability to form biofilm-like structures and to disrupt specific membranes.

Efficacy of cardiac rehabilitation with motion assistance from wearable cyborg hybrid assistive limb in patients with chronic heart failure: a randomized controlled trial

Background

Recent Cochrane Systematic Review suggested that the participation in cardiac rehabilitation is associated with approximately 20% lower cardiovascular mortality and morbidity. Exercise therapy is the key component of cardiac rehabilitation programs. In recent years, innovative technologies have been introduced into the field of rehabilitation, and a typical example is the wearable cyborg Hybrid Assistive Limb (HAL). The wearable cyborg HAL provides motion assistance based on detection of bioelectrical signals on the skin surface when muscle forces are generated. The lumbar-type HAL is expected to expand the therapeutic options for severe cardiac patients who have difficulty in performing usual cardiac rehabilitation programs, such as bicycle pedaling or walking.

Purpose

We aim to compare the efficacy of exercise therapy performed with motion assistance from a lumbar-type HAL versus conventional training (sit-to-stand exercise without HAL) in patients with chronic heart failure.

Methods

This clinical trial is a randomized, non-blinded, and controlled study. Twenty-eight heart failure patients (73.1±13.8 years) who have difficulty in walking at the usual walking speed of healthy subjects were randomly assigned to 2 groups (HAL group or control group) with a 1:1 allocation ratio and performed sit-to stand exercise either with HAL or without HAL for 5 to 30 minutes once a day, and 6 to 10 days during the study period. The brain natriuretic peptide (BNP), isometric knee extensor strength, standing ability (30-seconds chair-stand test: CS-30), short physical performance battery (SPPB) and 6-minute walking distance (6MWD) were measured before and after the completion of cardiac rehabilitation. Cardiac events such as death, re-hospitalization, myocardial infarction and worsening of angina pectoris and heart failure during 1 year after discharge were evaluated.

Results

There was no significant difference in the number of days of exercise therapy between the two groups. BNP, SPPB and 6MWD were improved in both groups. In the HAL group, the isometric knee extensor strength (0.29±0.11 vs 0.35±0.11 kgf/kg, p=0.003) significantly improved and CS-30 (5.5±5.1 vs 8.2±5.3, p=0.054) tended to improve. However, in the control group, either the isometric knee extensor strength (0.35±0.11 vs 0.36±0.14 kgf/kg, p=0.424) or CS-30 (6.0±4.3 vs 9.2±6.2, p=0.075) did not significantly change. HAL group showed significantly more improvement in the isometric knee extensor strength than control group (p=0.045). Cardiac events occurred in 20% in the HAL group and 43% in the control group.

Conclusion

The improvement in isometric knee extensor strength with the assistance from lumbar-type HAL suggests that exercise therapy using this device may be useful in chronic heart failure patients with flail or sarcopenia, a strong poor prognostic factor in these patients.

Funding Acknowledgement

Type of funding source: Public grant(s) – National budget only. Main funding source(s): This work was supported in part by a grant-in-aid for Scientific Research from the Ministry of Education, Science, and Culture of Japan (JSPS KAKENHI grant number JP17K09485) and funded by the ImPACT Program of the Council for Science, Technology and Innovation (Cabinet Office, Government of Japan) (grant number 2017-PM05-03-01).

Self- and Cross-Seeding on α-Synuclein Fibril Growth Kinetics and Structure Observed by High-Speed Atomic Force Microscopy

Fibril formation is an obligatory process in amyloid diseases and is characterized by nucleation and elongation phases that result in the formation of long filaments with cross-β sheet structure. The kinetics of this process, as well as that of secondary nucleation, is controlled by a variety of factors, including nucleus (seed) structure, monomer conformation, and biochemical milieu. Some fibrillar amyloid assemblies act as prions, replicating themselves from protein monomers templated by existing prion seeds. Prion strains, which are characterized by distinct physicochemical and pathologic properties, may also form due to perturbation of the templating process within the susceptible organism. Understanding the types and effects of perturbations occurring during the development and progression of Parkinson's disease is an area requiring more study. Here, we used high-speed atomic force microscopy to determine the kinetics and structural dynamics of α-synuclein fibril elongation initiated by self-seeding or cross-seeding of wild-type (WT) or mutant α-synuclein with WT or mutant α-synuclein seeds. We found that cross-seeding modulated not only elongation rates but also the structures of the growing fibrils. Some fibrils produced in this manner had structures distinct from their "parent" seeds. In other cases, cross-seeding was not observed at all. These findings suggest that α-synuclein sequence variants can produce different types of strains by self- or cross-seeding. Perpetuation of specific strains then would depend on the relative rates of fibril growth and the relative stabilities of the fibrils formed by each strain.

Rad50 zinc hook functions as a constitutive dimerization module interchangeable with SMC hinge

The human Mre11/Rad50 complex is one of the key factors in genome maintenance pathways. Previous nanoscale imaging by atomic force microscopy (AFM) showed that the ring-like structure of the human Mre11/Rad50 complex transiently opens at the zinc hook of Rad50. However, imaging of the human Mre11/Rad50 complex by high-speed AFM shows that the Rad50 coiled-coil arms are consistently bridged by the dimerized hooks while the Mre11/Rad50 ring opens by disconnecting the head domains; resembling other SMC proteins such as cohesin or condensin. These architectural features are conserved in the yeast and bacterial Mre11/Rad50 complexes. Yeast strains harboring the chimeric Mre11/Rad50 complex containing the SMC hinge of bacterial condensin MukB instead of the RAD50 hook properly functions in DNA repair. We propose that the basic role of the Rad50 hook is similar to that of the SMC hinge, which serves as rather stable dimerization interface.

Polymerization of Oxidized DJ-1 via Noncovalent and Covalent Binding: Significance of Disulfide Bond Formation

The reactive cysteine residue at position 106 (Cys106) of DJ-1 is preferentially oxidized under oxidative stress, generating oxidized DJ-1 (oxDJ-1). Oxidation of Cys106 to sulfinic acid changes the biologic action of DJ-1 and increases its cytoprotective properties. The similar activation step is known in peroxiredoxins (Prxs), in which oxidation of reactive Cys to sulfinic acid induces polymerization of Prxs and changes its enzyme characteristic from peroxidase to molecular chaperone. In the present study, oxDJ-1 was prepared and its polymerization and related amino acid residues were investigated. We found that oxDJ-1 formed a characteristic polymer with disulfide bonds and with noncovalent and covalent binding other than disulfide. The physiological concentration of glutathione resolved the polymer form of oxDJ-1, and glutathionylation of other two Cys residues, such as Cys 46 and 53, was detected. Mutant analysis indicated the necessity not only of Cys106 but also of Cys46 for the polymer formation. The cellular experiment demonstrated that the electrophilic quinone treatment induced a high-molecular-weight complex containing oxDJ-1. Dynamic polymerization of oxDJ-1 with a ring and a stacked structure was observed by an atomic force microscope. Collectively, these results clearly demonstrated the characteristic polymer formation of oxDJ-1 with a disulfide bond and noncovalent and covalent binding other than disulfide, which might be related to the biologic function of oxDJ-1.

Author Correction: PtdIns(3,5)P2 mediates root hair shank hardening in Arabidopsis

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

PtdIns(3,5)P2 mediates root hair shank hardening in Arabidopsis

Root hairs elongate by tip growth and simultaneously harden the shank by constructing the inner secondary cell wall layer. While much is known about the process of tip growth¹, almost nothing is known about the mechanism by which root hairs harden the shank. Here we show that phosphatidylinositol-3,5-bisphosphate (PtdIns(3,5)P₂), the enzymatic product of FORMATION OF APLOID AND BINUCLEATE CELLS 1 (FAB1), is involved in the hardening of the shank in root hairs in Arabidopsis. FAB1 and PtdIns(3,5)P₂ localize to the plasma membrane along the shank of growing root hairs. By contrast, phosphatidylinositol 4-phosphate 5-kinase 3 (PIP5K3) and PtdIns(4,5)P₂ localize to the apex of the root hair where they are required for tip growth. Reduction of FAB1 function results in the formation of wavy root hairs while those of the wild type are straight. The localization of FAB1 in the plasma membrane of the root hair shank requires the activity of Rho-related GTPases from plants 10 (ROP10) and localization of ROP10 requires FAB1 activity. Computational modelling of root hair morphogenesis successfully reproduces the wavy root hair phenotype. Taken together, these data demonstrate that root hair shank hardening requires PtdIns(3,5)P₂/ROP10 signalling.

Single-Unit Imaging of Membrane Protein-Embedded Nanodiscs from Two Oriented Sides by High-Speed Atomic Force Microscopy

Membrane proteins play important roles in various cellular functions. To analyze membrane proteins, nanodisc technology using membrane scaffold proteins allows single membrane protein units to be embedded into the lipid bilayer disc without detergents. Recent advancements in high-speed atomic force microscopy (HS-AFM) have enabled us to monitor the real-time dynamics of proteins in solution at the nanometer scale. In this study, we report HS-AFM imaging of membrane proteins reconstituted into nanodiscs using two membrane protein complexes, SecYEG complex and MgtE dimer. The observed images showed single particles of membrane protein-embedded nanodiscs in an end-up orientation whereby the membrane was fixed parallel to the supporting solid surface and in a side-on orientation whereby the membrane plane was vertically fixed to the solid surface, enabling the elucidation of domain fluctuations in membrane proteins. This technique provides a basic method for the high-resolution imaging of single membrane proteins by HS-AFM.

Negatively Charged Lipids Are Essential for Functional and Structural Switch of Human 2-Cys Peroxiredoxin II

The function of ubiquitous 2-Cys peroxiredoxins (Prxs) can be converted alternatively from peroxidases to molecular chaperones. This conversion has been reported to occur by the formation of high-molecular-weight (HMW) complexes upon overoxidation of or ATP/ADP binding to 2-Cys Prxs, but its mechanism is not well understood. Here, we show that upon binding to phosphatidylserine or phosphatidylglycerol dimeric human 2-Cys PrxII (hPrxII) is assembled to trefoil-shaped small oligomers (possibly hexamers) with full chaperone and null peroxidase activities. Spherical HMW complexes are formed, only when phosphatidylserine or phosphatidylglycerol is bound to overoxidized or ATP/ADP-bound hPrxII. The spherical HMW complexes are lipid vesicles covered with trefoil-shaped oligomers arranged in a hexagonal lattice pattern. Thus, these lipids with a net negative charge, which can be supplied by increased membrane trafficking under oxidative stress, are essential for the structural and functional switch of hPrxII and possibly most 2-Cys Prxs.

Intramolecular interaction suggests an autosuppression mechanism for the innate immune adaptor protein MyD88

An autosupression of MyD88 is regulated by the intramolecular interaction between TIR_MyD88 and DD_MyD88.

Ubiquitin chain specificities of E6AP E3 ligase and its HECT domain

Ubiquitination of target proteins is accomplished by isopeptide bond formation between the carboxy group of the C-terminal glycine (Gly) residue of ubiquitin (Ub) and the ɛ-amino group of lysine (Lys) on the target proteins. The formation of an isopeptide bond between Ubs that gives rise to a poly-Ub chain on the target proteins and the types of poly-Ub chains formed depend on which of the seven Lys residues or N-terminal methionine (Met) residue on Ub is used for chain elongation. To understand the linkage specificity mechanism of Ub chains on E3, the previous study established an assay to monitor the formation of a free diubiquitin chain (Ub₂ chain synthesis assay) by HECT type E3 ligase. In this study, we investigated Ub₂ chain specificity using E6AP HECT domain. We here demonstrate the importance of the N-terminal domain of full length E6AP for Ub₂ chain specificity.

Demonstration of correlative atomic force and transmission electron microscopy using actin cytoskeleton

In this study, we present a new technique called correlative atomic force and transmission electron microscopy (correlative AFM/TEM) in which a targeted region of a sample can be observed under AFM and TEM. The ultimate goal of developing this new technique is to provide a technical platform to expand the fields of AFM application to complex biological systems such as cell extracts. Recent advances in the time resolution of AFM have enabled detailed observation of the dynamic nature of biomolecules. However, specifying molecular species, by AFM alone, remains a challenge. Here, we demonstrate correlative AFM/TEM, using actin filaments as a test sample, and further show that immuno-electron microscopy (immuno-EM), to specify molecules, can be integrated into this technique. Therefore, it is now possible to specify molecules, captured under AFM, by subsequent observation using immuno-EM. In conclusion, correlative AFM/TEM can be a versatile method to investigate complex biological systems at the molecular level.

Impact of hospital volume on risk-adjusted mortality following oesophagectomy in Japan

Background

Previous studies have reported that patients undergoing oesophagectomy in high-volume hospitals experience lower mortality rates. However, there has been ongoing discussion regarding the validity of evidence for this association. The purpose of this study was to investigate the relationship between hospital volume and risk-adjusted mortality following oesophagectomy in Japan, using a nationwide web-based database.

Methods

The study included patients registered in the database as having undergone oesophagectomy with reconstruction between 2011 and 2013. Outcome measures were 30-day and operative mortality rates. Logistic regression analysis was used to adjust for hospital volume, surgeon volume and risk factors for mortality after oesophagectomy.

Results

A total of 16 556 oesophagectomies at 988 hospitals were included; the overall unadjusted 30-day and operative mortality rates were 1·1 and 3·0 per cent respectively. The unadjusted operative mortality rate in hospitals performing fewer than ten procedures per year (5·1 per cent) was more than three times higher than that in hospitals conducting 30 or more procedures annually (1·5 per cent). Multivariable models indicated that hospital volume had a significant effect on 30-day (odds ratio 0·88 per 10-patient increase; P = 0·012) and operative (odds ratio 0·86 per 10-patient increase; P < 0·001) mortality.

Conclusion

In Japan, high-volume hospitals had lower risk-adjusted 30-day and operative mortality rates following oesophagectomy compared with low-volume hospitals.

High-speed atomic force microscopy reveals strongly polarized movement of clostridial collagenase along collagen fibrils

Bacterial collagenases involved in donor infection are widely applied in many fields due to their high activity and specificity; however, little is known regarding the mechanisms by which bacterial collagenases degrade insoluble collagen in host tissues. Using high-speed atomic force microscopy, we simultaneously visualized the hierarchical structure of collagen fibrils and the movement of a representative bacterial collagenase, Clostridium histolyticum type I collagenase (ColG), to determine the relationship between collagen structure and collagenase movement. Notably, ColG moved ~14.5 nm toward the collagen N terminus in ~3.8 s in a manner dependent on a catalytic zinc ion. While ColG was engaged, collagen molecules were not only degraded but also occasionally rearranged to thicken neighboring collagen fibrils. Importantly, we found a similarity of relationship between the enzyme-substrate interface structure and enzyme migration in collagen-collagenase and DNA-nuclease systems, which share a helical substrate structure, suggesting a common strategy in enzyme evolution.

An autopsied case of neuromyelitis optica with a large cavitary cerebral lesion

We report a case of neuromyelitis optica (NMO) with a large cerebral lesion. The patient had an episode of fever and consciousness disturbance with a tumefactive frontal white matter lesion at age 43, and then repeated bilateral optic neuritis and transverse myelitis until she died at age 63. Histopathological examinations revealed that marked tissue destruction, cavities and inflammatory changes typical of NMO were seen in the cerebrum as well as the optic nerves and spinal cord. This is the first autopsied case of NMO with a tumefactive cerebral lesion that later became cavitary.

Oxidation of a Cysteine Residue in Elongation Factor EF-Tu Reversibly Inhibits Translation in the Cyanobacterium Synechocystis sp. PCC 6803

Translational elongation is susceptible to inactivation by reactive oxygen species (ROS) in the cyanobacterium Synechocystis sp. PCC 6803, and elongation factor G has been identified as a target of oxidation by ROS. In the present study we examined the sensitivity to oxidation by ROS of another elongation factor, EF-Tu. The structure of EF-Tu changes dramatically depending on the bound nucleotide. Therefore, we investigated the sensitivity to oxidation in vitro of GTP- and GDP-bound EF-Tu as well as that of nucleotide-free EF-Tu. Assays of translational activity with a reconstituted translation system from Escherichia coli revealed that GTP-bound and nucleotide-free EF-Tu were sensitive to oxidation by H2O2, whereas GDP-bound EF-Tu was resistant to H2O2. The inactivation of EF-Tu was the result of oxidation of Cys-82, a single cysteine residue, and subsequent formation of both an intermolecular disulfide bond and sulfenic acid. Replacement of Cys-82 with serine rendered EF-Tu resistant to inactivation by H2O2, confirming that Cys-82 was a target of oxidation. Furthermore, oxidized EF-Tu was reduced and reactivated by thioredoxin. Gel-filtration chromatography revealed that some of the oxidized nucleotide-free EF-Tu formed large complexes of >30 molecules. Atomic force microscopy revealed that such large complexes dissociated into several smaller aggregates upon the addition of dithiothreitol. Immunological analysis of the redox state of EF-Tu in vivo showed that levels of oxidized EF-Tu increased under strong light. Thus, resembling elongation factor G, EF-Tu appears to be sensitive to ROS via oxidation of a cysteine residue, and its inactivation might be reversed in a redox-dependent manner.

Redox regulation of CF1-ATPase involves interplay between the γ-subunit neck region and the turn region of the βDELSEED-loop

The soluble F1 complex of ATP synthase (FoF1) is capable of ATP hydrolysis, accomplished by the minimum catalytic core subunits α3β3γ. A special feature of cyanobacterial F1 and chloroplast F1 (CF1) is an amino acid sequence inserted in the γ-subunit. The insertion is extended slightly into the CF1 enzyme containing two additional cysteines for regulation of ATPase activity via thiol modulation. This molecular switch was transferred to a chimeric F1 by inserting the cysteine-containing fragment from spinach CF1 into a cyanobacterial γ-subunit [Y. Kim et al., redox regulation of rotation of the cyanobacterial F1-ATPase containing thiol regulation switch, J Biol Chem, 286 (2011) 9071-9078]. Under oxidizing conditions, the obtained F1 tends to lapse into an ADP-inhibited state, a common regulation mechanism to prevent wasteful ATP hydrolysis under unfavorable circumstances. However, the information flow between thiol modulation sites on the γ-subunit and catalytic sites on the β-subunits remains unclear. Here, we clarified a possible interplay for the CF1-ATPase redox regulation between structural elements of the βDELSEED-loop and the γ-subunit neck region, i.e., the most convex part of the α-helical γ-termini. Critical residues were assigned on the β-subunit, which received the conformation change signal produced by disulfide/dithiol formation on the γ-subunit. Mutant response to the ATPase redox regulation ranged from lost to hypersensitive. Furthermore, mutant cross-link experiments and inversion of redox regulation indicated that the γ-redox state might modulate the subunit interface via reorientation of the βDELSEED motif region.

Reversible control of F(1)-ATPase rotational motion using a photochromic ATP analog at the single molecule level

Motor enzymes such as F1-ATPase and kinesin utilize energy from ATP for their motion. Molecular motions of these enzymes are critical to their catalytic mechanisms and were analyzed thoroughly using a single molecule observation technique. As a tool to analyze and control the ATP-driven motor enzyme motion, we recently synthesized a photoresponsive ATP analog with a p-tert-butylazobenzene tethered to the 2' position of the ribose ring. Using cis/trans isomerization of the azobenzene moiety, we achieved a successful reversible photochromic control over a kinesin-microtubule system in an in vitro motility assay. Here we succeeded to control the hydrolytic activity and rotation of the rotary motor enzyme, F1-ATPase, using this photosensitive ATP analog. Subsequent single molecule observations indicated a unique pause occurring at the ATP binding angle position in the presence of cis form of the analog.

Kinetics of the catalytic cracking of naphtha over ZSM-5 zeolite: effect of reduced crystal size on the reaction of naphthenes

The catalytic cracking of model naphthenes over ZSM-5 zeolites of different crystal sizes was examined at reaction temperatures ranging from 748 to 923 K under atmospheric pressure, focusing on the associated reaction rate constants and activation energies.

The chloroplast ATP synthase features the characteristic redox regulation machinery

SIGNIFICANCE

Regulation of the activity of the chloroplast ATP synthase is largely accomplished by the chloroplast thioredoxin system, the main redox regulation system in chloroplasts, which is directly coupled to the photosynthetic reaction. We review the current understanding of the redox regulation system of the chloroplast ATP synthase.

RECENT ADVANCES

The thioredoxin-targeted portion of the ATP synthase consists of two cysteines located on the central axis subunit γ. The redox state of these two cysteines is under the influence of chloroplast thioredoxin, which directly controls rotation during catalysis by inducing a conformational change in this subunit. The molecular mechanism of redox regulation of the chloroplast ATP synthase has recently been determined.

CRITICAL ISSUES

Regulation of the activity of the chloroplast ATP synthase is critical in driving efficiency into the ATP synthesis reaction in chloroplasts.

FUTURE DIRECTIONS

The molecular architecture of the chloroplast ATP synthase, which confers redox regulatory properties requires further investigation, in light of the molecular structure of the enzyme complex as well as the physiological significance of the regulation system.

Common evolutionary origin for the rotor domain of rotary ATPases and flagellar protein export apparatus

The V₁- and F₁- rotary ATPases contain a rotor that rotates against a catalytic A₃B₃ or α₃β₃ stator. The rotor F₁-γ or V₁-DF is composed of both anti-parallel coiled coil and globular-loop parts. The bacterial flagellar type III export apparatus contains a V₁/F₁-like ATPase ring structure composed of FliI₆ homo-hexamer and FliJ which adopts an anti-parallel coiled coil structure without the globular-loop part. Here we report that FliJ of Salmonella enterica serovar Typhimurium shows a rotor like function in Thermus thermophilus A₃B₃ based on both biochemical and structural analysis. Single molecular analysis indicates that an anti-parallel coiled-coil structure protein (FliJ structure protein) functions as a rotor in A₃B₃. A rotary ATPase possessing an F₁-γ-like protein generated by fusion of the D and F subunits of V₁ rotates, suggesting F₁-γ could be the result of a fusion of the genes encoding two separate rotor subunits. Together with sequence comparison among the globular part proteins, the data strongly suggest that the rotor domains of the rotary ATPases and the flagellar export apparatus share a common evolutionary origin.

Nano-scale alignment of proteins on a flexible DNA backbone

Nano-scale alignment of several proteins with freedom of motion is equivalent to an enormous increase in effective local concentration of proteins and will enable otherwise impossible weak and/or cooperative associations between them or with their ligands. For this purpose, a DNA backbone made of six oligodeoxynucleotide (ODN) chains is designed in which five double-stranded segments are connected by four single-stranded flexible linkers. A desired protein with an introduced cysteine is connected covalently to the 5'-end of azido-ODN by catalyst-free click chemistry. Then, six protein-ODN conjugates are assembled with their complementary nucleotide sequences into a single multi-protein-DNA complex, and six proteins are aligned along the DNA backbone. Flexible alignment of proteins is directly observed by high-speed AFM imaging, and association of proteins with weak interaction is demonstrated by fluorescence resonance energy transfer between aligned proteins.

Abstract P6-04-17: The androgen metabolite-dependent growth in hormone receptor positive breast cancer as a novel aromatase inhibitor-resistance mechanism

Introduction: Aromatase inhibitors (AIs) have been reported to exert their anti-proliferative effects not only by reducing the production of estrogens but also by unmasking the inhibitory effect of androgens such as testosterone (TS) or dihydrotestosterone (DHT) in postmenopausal women with hormone receptor-positive breast cancer. The behavior of androgens in AI-resistance mechanisms is not sufficiently understood. 5α-androstane-3β,17β-diol (3β-diol) generated from DHT by 3β-hydroxysteroid dehydrogenase type 1 (3β-HSD type 1: HSD3B1) has androgenic activity and substantial estrogenic activity, representing a potential mechanism of AI resistance.

Methods: To investigate these issues, ERE-GFP-transfected MCF-7-E10 cells were cultured for 3 months under steroid-depleted, TS-supplemented conditions which is the similar as the AI treatment. Among the surviving cells, two stable variants that show ER activity depending on androgen metabolites were selected as AD-EDR (androgen metabolite-dependent and estrogen depletion-resistant) by monitoring GFP expression. Using these cell lines, we investigated the process of adaptation to androgen-abundant conditions and the role of androgens in AI-resistance mechanisms.

Results: AD-EDR cell lines showed increased growth and induction of estrogen-responsive genes rather than androgen-responsive genes by androgens or 3β-diol. Further analysis revealed increased expressions of HSD3B1 and reduced expression of androgen receptor (AR) in these cell lines. In parental MCF-7-E10 cells, ectopic expression of HSD3B1 or inhibition of AR resulted in adaptation to estrogen-deprived and androgen-abundant conditions. In coculture with stromal cells replicating the local estrogen production from androgen, AD-EDR cell lines showed AI resistance compared with parental MCF-7-E10 cells. Immunohistochemistry and real-time PCR analyses on 9 pairs of primary and recurrent tissue samples from AI-resistant breast cancer revealed the decrease of AR protein expression in all cases and increase of HSD3B1 mRNA expression in 5.

Conclusion: In the present study, we successfully cloned two stable variants that show ER activity depending on androgen metabolites. Investigation of these cell lines suggested that the increased function of 3β-HSD type 1 and reduced function of AR contribute to AI resistance by enhancing the androgen metabolite-dependent growth and reducing the inhibitory effect of androgens. Our data of clinical samples suggest that this mechanism also acts as an AI-resistance in clinical breast cancer in some cases.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P6-04-17.

A conformational change of the γ subunit indirectly regulates the activity of cyanobacterial F1-ATPase

The central shaft of the catalytic core of ATP synthase, the γ subunit consists of a coiled-coil structure of N- and C-terminal α-helices, and a globular domain. The γ subunit of cyanobacterial and chloroplast ATP synthase has a unique 30-40-amino acid insertion within the globular domain. We recently prepared the insertion-removed α(3)β(3)γ complex of cyanobacterial ATP synthase (Sunamura, E., Konno, H., Imashimizu-Kobayashi, M., and Hisabori, T. (2010) Plant Cell Physiol. 51, 855-865). Although the insertion is thought to be located in the periphery of the complex and far from catalytic sites, the mutant complex shows a remarkable increase in ATP hydrolysis activity due to a reduced tendency to lapse into ADP inhibition. We postulated that removal of the insertion affects the activity via a conformational change of two central α-helices in γ. To examine this hypothesis, we prepared a mutant complex that can lock the relative position of two central α-helices to each other by way of a disulfide bond formation. The mutant obtained showed a significant change in ATP hydrolysis activity caused by this restriction. The highly active locked complex was insensitive to N-dimethyldodecylamine-N-oxide, suggesting that the complex is resistant to ADP inhibition. In addition, the lock affected ε inhibition. In contrast, the change in activity caused by removal of the γ insertion was independent from the conformational restriction of the central axis component. These results imply that the global conformational change of the γ subunit indirectly regulates complex activity by changing both ADP inhibition and ε inhibition.

Thiol modulation of the chloroplast ATP synthase is dependent on the energization of thylakoid membranes

Thiol modulation of the chloroplast ATP synthase γ subunit has been recognized as an important regulatory system for the activation of ATP hydrolysis activity, although the physiological significance of this regulation system remains poorly characterized. Since the membrane potential required by this enzyme to initiate ATP synthesis for the reduced enzyme is lower than that needed for the oxidized form, reduction of this enzyme was interpreted as effective regulation for efficient photophosphorylation. However, no concrete evidence has been obtained to date relating to the timing and mode of chloroplast ATP synthase reduction and oxidation in green plants. In this study, thorough analysis of the redox state of regulatory cysteines of the chloroplast ATP synthase γ subunit in intact chloroplasts and leaves shows that thiol modulation of this enzyme is pivotal in prohibiting futile ATP hydrolysis activity in the dark. However, the physiological importance of efficient ATP synthesis driven by the reduced enzyme in the light could not be demonstrated. In addition, we investigated the significance of the electrochemical proton gradient in reducing the γ subunit by the reduced form of thioredoxin in chloroplasts, providing strong insights into the molecular mechanisms underlying the formation and reduction of the disulfide bond on the γ subunit in vivo.

Influence of age and gender on human lymphatic pumping pressure in the leg

Lymph transportation is controlled, at least in part, by the intrinsic pumping of lymphatic vessels. The objectives of this study were to evaluate the influences of age and gender on leg lymphatic pumping pressure. A total of 399 subjects between the ages of 20 and 91 years (199 males and 200 females) volunteered to participate in this study. Lymphatic pumping was measured in 798 legs of the 399 participants. Indocyanine green (ICG) fluorescence lymphography was performed, and the real-time fluorescence images of lymph propulsion were obtained in a sitting position using an infrared-light camera system. A custom-made transparent sphygmomanometer cuff was wrapped around the lower leg and connected to a standard mercury sphygmomanometer. The cuff was inflated, and then gradually deflated until the fluorescent dye exceeded the upper border of the cuff. Lymph pumping pressure was defined as the value of the cuff pressure when the dye exceeded the upper border of the cuff. There was a significant correlation between the leg lymphatic pumping and age: r = -0.34 (p < 0.0001). Comparison of lymphatic pumping between males and females indicated that the age-related decrease in lymphatic pumping pressure was more marked in females of postmenopausal age.

The catalytic mechanism of dye-decolorizing peroxidase DyP may require the swinging movement of an aspartic acid residue

The dye-decolorizing peroxidase (DyP)-type peroxidase family is a unique heme peroxidase family. The primary and tertiary structures of this family are obviously different from those of other heme peroxidases. However, the details of the structure-function relationships of this family remain poorly understood. We show four high-resolution structures of DyP (EC1.11.1.19), which is representative of this family: the native DyP (1.40 Å), the D171N mutant DyP (1.42 Å), the native DyP complexed with cyanide (1.45 Å), and the D171N mutant DyP associated with cyanide (1.40 Å). These structures contain four amino acids forming the binding pocket for hydrogen peroxide, and they are remarkably conserved in this family. Moreover, these structures show that OD2 of Asp171 accepts a proton from hydrogen peroxide in compound I formation, and that OD2 can swing to the appropriate position in response to the ligand for heme iron. On the basis of these results, we propose a swing mechanism in compound I formation. When DyP reacts with hydrogen peroxide, OD2 swings towards an optimal position to accept the proton from hydrogen peroxide bound to the heme iron.