Actin capping protein and its inhibitor CARMIL: how intrinsically disordered regions function

The actin capping protein (CP) tightly binds to the barbed end of actin filaments to block further elongation. The β-tentacle in CP is an important region that ensures stable interaction with actin filaments. CARMIL inhibits the interaction of CP with actin filaments via the C-terminal portion containing the CP-binding motif, located in an intrinsically disordered region. We have proposed an allosteric inhibition model in which CARMIL suppresses CP by the population shift mechanism. Here, we solved a crystal structure of CP in complex with a CARMIL-derived peptide, CA32. The new structure clearly represents the α-helical form of the β-tentacle that was invisible in other CP/CARMIL peptide complex structures. In addition, we exhaustively performed a normal mode analysis with the elastic network model on all available crystal structures of the CP/CARMIL peptide complexes, including the new structure. We concluded that the CP-binding motif is necessary and sufficient for altering the fluctuation of CP, which is essential for attenuating the barbed-end-capping activity along the population shift mechanism. The roles and functions of the β-tentacle and the CP-binding motif are discussed in terms of their intrinsically disordered nature.     

Generation of a conditional null allele of Lbx1

The homeobox gene Lbx1 not only plays critical roles in myogenesis and neurogenesis during embryonic development but is also expressed in activated satellite cells of adult mice. To address the potential postnatal functions of Lbx1, we generated conditional Lbx1-null mice using the Cre-loxP system. We generated a mouse in which Exon 2 of Lbx1 was floxed (Lbx1flox/flox), followed by cross-breeding between the Lbx1flox/flox mouse and either a transgenic mouse where a tamoxifen-inducible Cre-recombinase (Cre) was ubiquitously expressed, or a Myf5Cre mouse where Cre was inserted into the Myf5 locus. In both Lbx1-null mouse lines generated, Pax3-expressing limb muscle precursor cells were seriously reduced during embryonic development and eventually the limb extensor muscles were lost after birth. Since the conditional Lbx1-null mice generated were viable for a prolonged time, they will be useful in the investigation of Lbx1 function throughout the lifespan of the mouse.     

Structural insight into the rotational switching mechanism of the bacterial flagellar motor

The bacterial flagellar motor can rotate either clockwise (CW) or counterclockwise (CCW). Three flagellar proteins, FliG, FliM, and FliN, are required for rapid switching between the CW and CCW directions. Switching is achieved by a conformational change in FliG induced by the binding of a chemotaxis signaling protein, phospho-CheY, to FliM and FliN. FliG consists of three domains, FliG(N), FliG(M), and FliG(C), and forms a ring on the cytoplasmic face of the MS ring of the flagellar basal body. Crystal structures have been reported for the FliG(MC) domains of Thermotoga maritima, which consist of the FliG(M) and FliG(C) domains and a helix E that connects these two domains, and full-length FliG of Aquifex aeolicus. However, the basis for the switching mechanism is based only on previously obtained genetic data and is hence rather indirect. We characterized a CW-biased mutant (fliG(ΔPAA)) of Salmonella enterica by direct observation of rotation of a single motor at high temporal and spatial resolution. We also determined the crystal structure of the FliG(MC) domains of an equivalent deletion mutant variant of T. maritima (fliG(ΔPEV)). The FliG(ΔPAA) motor produced torque at wild-type levels under a wide range of external load conditions. The wild-type motors rotated exclusively in the CCW direction under our experimental conditions, whereas the mutant motors rotated only in the CW direction. This result suggests that wild-type FliG is more stable in the CCW state than in the CW state, whereas FliG(ΔPAA) is more stable in the CW state than in the CCW state. The structure of the TM-FliG(MC)(ΔPEV) revealed that extremely CW-biased rotation was caused by a conformational change in helix E. Although the arrangement of FliG(C) relative to FliG(M) in a single molecule was different among the three crystals, a conserved FliG(M)-FliG(C) unit was observed in all three of them. We suggest that the conserved FliG(M)-FliG(C) unit is the basic functional element in the rotor ring and that the PAA deletion induces a conformational change in a hinge-loop between FliG(M) and helix E to achieve the CW state of the FliG ring. We also propose a novel model for the arrangement of FliG subunits within the motor. The model is in agreement with the previous mutational and cross-linking experiments and explains the cooperative switching mechanism of the flagellar motor.     

An extensive analysis of R2R3-MYB regulatory genes from Fagus crenata

Using pairs of degenerate primers, we conducted a polymerase chain reaction to amplify the partial R2R3 domains of a majority of the R2R3-MYB family genes from Fagus crenata and identified a total of 85 independent gene fragments. By phylogenetic analysis of the deduced amino acid sequences, we found that many of the beech genes clustered with members from Arabidopsis, suggesting that these members represent beech orthologs of Arabidopsis. Some of the orthologous relationships became more evident when the complete gene structures were compared. Further, a large number of genes formed an additional and expanding cluster, independent from the other subgroups. These members were further compared with the Populus and Vitis family genes. In the epidermal cell fate clade, expansion of the beech family genes was comparable with those of the Populus and Vitis families, but the number of genes present in every subclade fluctuated extensively. Beech genes were abundant in the general flavonoid pathway regulation and TT2-related subclades; no beech gene was included in the anthocyanin-related subclade. Further analysis of the newly amplified regulatory genes to elucidate their functions may clarify the role of these genes in the evolution of plant species.     

Detailed structural analysis of lipids directly on tissue specimens using a MALDI-SpiralTOF-Reflectron TOF mass spectrometer

Direct tissue analysis using a novel tandem time-of-flight (TOF-TOF) mass spectrometer is described. This system consists of a matrix-assisted laser desorption/ionization ion source, a spiral ion trajectory TOF mass spectrometer "SpiralTOF (STOF)", a collision cell, and an offset parabolic reflectron (RTOF). The features of this system are high precursor ion selectivity due to a 17-m flight path length in STOF and elimination of post-source decay (PSD) ions. The acceleration energy is 20 keV, so that high-energy collision-induced dissociation (HE-CID) is possible. Elimination of PSD ions allows observation of the product ions inherent to the HE-CID process. By using this tandem TOF instrument, the product ion spectrum of lipids provided detailed structural information of fatty acid residues.     

Cell-to-cell heterogeneity in cortical tension specifies curvature of contact surfaces in Caenorhabditis elegans embryos

In the two-cell stage embryos of Caenorhabditis elegans, the contact surface of the two blastomeres forms a curve that bulges from the AB blastomere to the P₁ blastomere. This curve is a consequence of the high intracellular hydrostatic pressure of AB compared with that of P₁. However, the higher pressure in AB is intriguing because AB has a larger volume than P₁. In soap bubbles, which are a widely used model of cell shape, a larger bubble has lower pressure than a smaller bubble. Here, we reveal that the higher pressure in AB is mediated by its higher cortical tension. The cell fusion experiments confirmed that the curvature of the contact surface is related to the pressure difference between the cells. Chemical and genetic interferences showed that the pressure difference is mediated by actomyosin. Fluorescence imaging indicated that non-muscle myosin is enriched in the AB cortex. The cell killing experiments provided evidence that AB but not P₁ is responsible for the pressure difference. Computer simulation clarified that the cell-to-cell heterogeneity of cortical tensions is indispensable for explaining the pressure difference. This study demonstrates that heterogeneity in surface tension results in significant deviations of cell behavior compared to simple soap bubble models, and thus must be taken into consideration in understanding cell shape within embryos.     

Optical rheology of porcine sclera by birefringence imaging

Purpose

To investigate a relationship between birefringence and elasticity of porcine sclera ex vivo using polarization-sensitive optical coherence tomography (PS-OCT).

Methods

Elastic parameters and birefringence of 19 porcine eyes were measured. Four pieces of scleral strips which were parallel to the limbus, with a width of 4 mm, were dissected from the optic nerve head to the temporal side of each porcine eye. Birefringence of the sclera was measured with a prototype PS-OCT. The strain and force were measured with a uniaxial material tester as the sample was stretched with a speed of 1.8 mm/min after preconditioning. A derivative of the exponentially-fitted stress-strain curve at 0% strain was extracted as the tangent modulus. Power of exponential stress-strain function was also extracted from the fitting. To consider a net stiffness of sclera, structural stiffness was calculated as a product of tangent modulus and thickness. Correlations between birefringence and these elastic parameters were examined.

Results

Statistically significant correlations between birefringence and all of the elastic parameters were found at 2 central positions. Structural stiffness and power of exponential stress-strain function were correlated with birefringence at the position near the optic nerve head. No correlation was found at the position near the equator.

Conclusions

The evidence of correlations between birefringence and elasticity of sclera tested uniaxially was shown for the first time. This work may become a basis for in vivo measurement of scleral biomechanics using PS-OCT.     

Discrimination of genotoxic and non-genotoxic hepatocarcinogens by statistical analysis based on gene expression profiling in the mouse liver as determined by quantitative real-time PCR

The general aim of the present study is to discriminate between mouse genotoxic and non-genotoxic hepatocarcinogens via selected gene expression patterns in the liver as analyzed by quantitative real-time PCR (qPCR) and statistical analysis. qPCR was conducted on liver samples from groups of 5 male, 9-week-old B6C3F(1) mice, at 4 and 48h following a single intraperitoneal administration of chemicals. We quantified 35 genes selected from our previous DNA microarray studies using 12 different chemicals: 8 genotoxic hepatocarcinogens (2-acetylaminofluorene, 2,4-diaminotoluene, diisopropanolnitrosamine, 4-dimethylaminoazobenzene, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone, N-nitrosomorpholine, quinoline and urethane) and 4 non-genotoxic hepatocarcinogens (1,4-dichlorobenzene, dichlorodiphenyltrichloroethane, di(2-ethylhexyl)phthalate and furan). A considerable number of genes exhibited significant changes in their gene expression ratios (experimental group/control group) analyzed statistically by the Dunnett's test and Welch's t-test. Finally, we distinguished between the genotoxic and non-genotoxic hepatocarcinogens by statistical analysis using principal component analysis (PCA) of the gene expression profiles for 7 genes (Btg2, Ccnf, Ccng1, Lpr1, Mbd1, Phlda3 and Tubb2c) at 4h and for 12 genes (Aen, Bax, Btg2, Ccnf, Ccng1, Cdkn1a, Gdf15, Lrp1, Mbd1, Phlda3, Plk2 and Tubb2c) at 48h. Seven major biological processes were extracted from the gene ontology analysis: apoptosis, the cell cycle, cell proliferation, DNA damage, DNA repair, oncogenes and tumor suppression. The major, biologically relevant gene pathway suggested was the DNA damage response pathway, resulting from signal transduction by a p53-class mediator leading to the induction of apoptosis. Eight genes (Aen, Bax, Btg2, Ccng1, Cdkn1a, Gdf15, Phlda3 and Plk2) that are directly associated with Trp53 contributed to the PCA. The current findings demonstrate a successful discrimination between genotoxic and non-genotoxic hepatocarcinogens, using qPCR and PCA, on 12 genes associated with a Trp53-mediated signaling pathway for DNA damage response at 4 and 48 h after a single administration of chemicals.