Assembly of different length of polyubiquitins on the catalytic cysteine of E2 enzymes without E3 ligase; a novel application of non-reduced/reduced 2-dimensional electrophoresis

AbstractIn this study using non-reduced/reduced 2-dimensional electrophoresis (NR/R-2DE), we clearly demonstrated that E3-independent ubiquitination by Ube2K produced not only unanchored but also Ube2K-linked polyubiquitins through thioester and isopeptide bonds. E3-independent assembly of polyubiquitins on the catalytic cysteine of Ube2K strongly supports the possibility of ‘en bloc transfer’ for polyubiquitination. From the same analyses of E3-independent ubiquitination products by other E2s, we also found that different lengths of polyubiquitins were linked to different E2s through thioester bond; longer chains by Cdc34 like Ube2K, short chains by Ube2g2, and mono-ubiquitin by UbcH10. Our results suggest that E2s possess the different intrinsic catalytic activities for polyubiquitination

Precessing Jet and Large Dust Grains in the V380 Ori NE Star-forming Region

The V380 Ori NE bipolar outflow was imaged in the SiO and CO J = 1 - 0 lines, and dense cores in L1641 were observed in the 2.0-0.89 mm continuum. The highly collimated SiO jet shows point-symmetric oscillation patterns in both position and velocity, which suggests that the jet axis is precessing and the driving source may belong to a non-coplanar binary system. By considering the position and velocity variabilities together, accurate jet parameters were derived. The protostellar system is viewed nearly edge-on, and the jet has a flow speed of 35 km/s and a precession period of 1600 years. The CO outflow length gives a dynamical timescale of 6300 years, and the protostar must be extremely young. The inferred binary separation of 6-70 au implies that this protobinary system may have been formed through the disk instability process. The continuum spectra of L1641 dense cores indicate that the emission comes from dust, and the fits with modified blackbody functions give emissivity power indices of beta = 0.3-2.2. The emissivity index shows a positive correlation with the molecular line width, but no strong correlation with bolometric luminosity or temperature. V380 Ori NE has a particularly low value of beta = 0.3, which tentatively suggests the presence of millimeter-sized dust grains. Because the dust growth takes millions of years, much longer than the protostellar age, this core may have produced large grains in the starless core stage. HH 34 MMS and HH 147 MMS also have low emissivity indices.Comment: To appear in the Astrophysical Journal Supplement Serie

Mid-JJ CO Line Observations of Protostellar Outflows in the Orion Molecular Clouds

Ten protostellar outflows in the Orion molecular clouds were mapped in the $^{12}$CO/$^{13}$CO ${J=6\rightarrow5}$ and $^{12}$CO ${J=7\rightarrow6}$ lines. The maps of these mid-$J$ CO lines have an angular resolution of about 10$''$ and a typical field size of about 100$''$. Physical parameters of the molecular outflows were derived, including mass transfer rates, kinetic luminosities, and outflow forces. The outflow sample was expanded by re-analyzing archival data of nearby low-luminosity protostars, to cover a wide range of bolometric luminosities. Outflow parameters derived from other transitions of CO were compared. The mid-$J$ ($J_{\rm up} \approx 6$) and low-$J$ ($J_{\rm up} \leq 3$) CO line wings trace essentially the same outflow component. By contrast, the high-$J$ (up to $J_{\rm up} \approx 50$) line-emission luminosity of CO shows little correlation with the kinetic luminosity from the ${J=6\rightarrow5}$ line, which suggests that they trace distinct components. The low/mid-$J$ CO line wings trace long-term outflow behaviors while the high-$J$ CO lines are sensitive to short-term activities. The correlations between the outflow parameters and protostellar properties are presented, which shows that the strengths of molecular outflows increase with bolometric luminosity and envelope mass.Comment: 31 pages, 16 figures, Accepted for publication in ApJ

The JCMT Transient Survey : stochastic and secular variability of protostars and disks in the submillimeter region observed over 18 months

We analyze results from the first 18 months of monthly submillimeter monitoring of eight star-forming regions in the JCMT Transient Survey. In our search for stochastic variability in 1643 bright peaks, only the previously identified source, EC 53, shows behavior well above the expected measurement uncertainty. Another four sources—two disks and two protostars—show moderately enhanced standard deviations in brightness, as expected for stochastic variables. For the two protostars, this apparent variability is the result of single epochs that are much brighter than the mean. In our search for secular brightness variations that are linear in time, we measure the fractional brightness change per year for 150 bright peaks, 50 of which are protostellar. The ensemble distribution of slopes is well fit by a normal distribution with σ ~ 0.023. Most sources are not rapidly brightening or fading at submillimeter wavelengths. Comparison against time-randomized realizations shows that the width of the distribution is dominated by the uncertainty in the individual brightness measurements of the sources. A toy model for secular variability reveals that an underlying Gaussian distribution of linear fractional brightness change σ = 0.005 would be unobservable in the present sample, whereas an underlying distribution with σ = 0.02 is ruled out. Five protostellar sources, 10% of the protostellar sample, are found to have robust secular measures deviating from a constant flux. The sensitivity to secular brightness variations will improve significantly with a sample over a longer time duration, with an improvement by factor of two expected by the conclusion of our 36 month survey.Publisher PDFPeer reviewe

Sequence-dependent DNA condensation as a driving force of DNA phase separation

The physical properties of DNA have been suggested to play a central role in spatio-temporal organization of eukaryotic chromosomes. Experimental correlations have been established between the local nucleotide content of DNA and the frequency of inter- and intra-chromosomal contacts but the underlying physical mechanism remains unknown. Here, we combine fluorescence resonance energy transfer (FRET) measurements, precipitation assays, and molecular dynamics simulations to characterize the effect of DNA nucleotide content, sequence, and methylation on inter-DNA association and its correlation with DNA looping. First, we show that the strength of DNA condensation mediated by poly-lysine peptides as a reduced model of histone tails depends on the DNA???s global nucleotide content but also on the local nucleotide sequence, which turns out to be qualitatively same as the condensation by spermine. Next, we show that the presence and spatial arrangement of C5 methyl groups determines the strength of inter-DNA attraction, partially explaining why RNA resists condensation. Interestingly, multi-color single molecule FRET measurements reveal strong anti-correlation between DNA looping and DNA-DNA association, suggesting that a common biophysical mechanism underlies them. We propose that the differential affinity between DNA regions of varying sequence pattern may drive the phase separation of chromatin into chromosomal subdomains