The H4K20 demethylase DPY-21 regulates the dynamics of condensin DC binding

Condensin is a multi-subunit SMC complex that binds to and compacts chromosomes. Here we addressed the regulation of condensin binding dynamics using C. elegans condensin DC, which represses X chromosomes in hermaphrodites for dosage compensation. We established fluorescence recovery after photobleaching (FRAP) using the SMC4 homolog DPY-27 and showed that a well-characterized ATPase mutation abolishes its binding. Next, we performed FRAP in the background of several chromatin modifier mutants that cause varying degrees of X-chromosome derepression. The greatest effect was in a null mutant of the H4K20me2 demethylase DPY-21, where the mobile fraction of condensin DC reduced from ∼30% to 10%. In contrast, a catalytic mutant of dpy-21 did not regulate condensin DC mobility. Hi-C data in the dpy-21 null mutant showed little change compared to wild type, uncoupling Hi-C measured long-range DNA contacts from transcriptional repression of the X chromosomes. Together, our results indicate that DPY-21 has a non-catalytic role in regulating the dynamics of condensin DC binding, which is important for transcription repression.

Alteration of Fractionation and Bioavailability of Arsenic (As) in Paddy Soil under Transition from Aerobic to Anaerobic Conditions

The impact of the change from aerobic to anaerobic immersed soil conditions on arsenic (As) fractionation (Tessier’s method) and its bioavailability (ethylene diamine tetraacetic acid extractable) were assessed. As-contaminated paddy soils were tested by laboratory simulation experiments. The samples were aerobic, with 35-49 mg/kg of As at low bioavailability (<2%). Most As was distributed in the stable fraction (77%), followed by As bound to ferric and manganese oxide (17%) and organic compounds (5%), while the mobile fraction (exchangeable and mildly acid-soluble) was limited (1%). After one month under anaerobic simulation, redox potential reduced to less than zero (-32 to -124 mV). The stable fraction of As decreased (-17%), while the mobile fraction increased (+16%) and As bioavailability also increased (+26% total As). Increase in the As mobile fraction was associated with freshly precipitated compounds. The As content in the soil altered from a stable fraction to an available fraction when confined in an anaerobic environment for a long period. Results indicated that agricultural methods which promoted anaerobic conditions in As-contaminated soil should be avoided.

Geochemical fractions and indicators of sedimentation conditions in the Barents sea

Research results of geochemical fractions and distribution pattern of the major and trace elements in the sediment cores of the Barents Sea are presented. In the sediment core AMK- 5193, located in the central part of the sea, Al, Cr and Ni were detected predominantly in the lithogenic form (75−97% of the total content) throughout the core. A large or a noticeable portion (from 65% to 30% from total contents) of Pb, Cd, Cu, Ni, Co, Mn, and As was found to be accumulated due to hydrogenous processes, such as adsorption on amorphous Fe-Mn oxyhydroxides and clay particles. In the uppermost oxidized layer (0−6 cm) of St. AMK-5193, where the most intensive exchange processes between the solid and liquid phases of bottom sediments happen, a significant increase in the proportion of geochemically mobile fraction of most metals was found. In this part of the core, the maximum content of Fe and Mn in the form of authigenic oxy-hydroxides which serve an effective sorbent of most trace elements, including heavy metals, was recorded. At st. 5194, the downcore rythmic covariation of the Si/Al, Ti/Al and Fe/Al ratios reflecting contribution of terrigenous matrix, as well as Al/Ca ratio (indicator of physical and chemical weathering) was revealed. Moreover, the Al/Ca ratio exhibited an asynchronous change with the Si/Al and Fe/Al ratios. Also, the downcore variation in the Ti/Al ratio was opposite to that of Mn/Fe (an indicator of geochemically mobile fraction). Variation of the Ti/Zr ratio, reflecting the range of aerosol transport of clastic material, is weakly expressed in the AMK-5194 core, which supports the proximity of the terrigenous source.

Immobilization of Potentially Toxic Elements in Contaminated Soils Using Thermally Treated Natural Zeolite

Rehabilitation of contaminated soils is a complex and time-consuming procedure. One of the most cost-effective and easy-to-use soil remediation approaches is the use of amendments that stabilize the potential toxic elements (PTE) in soil by reducing their mobility and bioavailability. The stabilization of Cu, Pb, Zn, Cd, Co, Cr, Ni in a contaminated soil using 5% and 10% amendment with thermally treated natural zeolite was investigated using a sequential extraction procedure, contamination and environmental risk factors. The results showed that after amendment, the PTE concentration decreased in the exchangeable and reducible fractions and increased in the oxidizable and residual fractions. The highest immobilization effect, consisting in the decrease of exchangeable fractions with 69% was obtained in case of 10% zeolite amendment and 90 days of equilibration time for Pb; also, more than half of the mobile fraction was immobilized in case of Zn, Cu, and Co and about one third in case of Ni, Cr, and Cd. Generally, the immobilization effect of the 5% and 10% amendment is comparable, but a higher equilibration time enhanced the immobilization effect, especially in the case of Cd, Co, Cu, Pb, and Zn.

Methanol dynamics in H-ZSM-5 with Si/Al ratio of 25: a quasi-elastic neutron scattering (QENS) study

Methanol dynamics in zeolite H-ZSM-5 (Si/Al of 25) with a methanol loading of ~ 30 molecules per unit cell has been studied at 298, 323, 348 and 373 K by incoherent quasi-elastic neutron scattering (QENS). The elastic incoherent structure factor (EISF) reveals that the majority of methanol is immobile, in the range between 70 and 80%, depending on the measurement temperature. At 298 K, ≈ 20% methanol is mobile on the instrumental timescale, exhibiting isotropic rotational dynamics with a rotational diffusion coefficient (DR) of 4.75 × 1010 s−1. Upon increasing the measurement temperature from 298 to 323 K, the nature of the methanol dynamics changes from rotational to translational diffusion dynamics. Similar translational diffusion rates are measured at 348 and 373 K, though with a larger mobile fraction as temperature increases. The translational diffusion is characterised as jump diffusion confined to a sphere with a radius close to that of a ZSM-5 channel. The diffusion coefficients may be calculated using either the Volino–Dianoux (VD) model of diffusion confined to a sphere, or the Chudley–Elliot (CE) jump diffusion model. The VD model gives rise to a self-diffusion co-efficient (Ds) of methanol in the range of 7.8–8.4 × 10–10 m2 s−1. The CE model gives a Ds of around 1.2 (± 0.1) × 10–9 m2 s−1 with a jump distance of 2.8 (either + 0.15 or − 0.1) Å and a residence time (τ) of ~ 10.8 (either + 0.1 or − 0.2) ps. A correlation between the present and earlier studies that report methanol dynamics in H-ZSM-5 with Si/Al of 36 is made, suggesting that with increasing Si/Al ratio, the mobile fraction of methanol increases while DR decreases.

Myosin VI regulates ciliogenesis by promoting the turnover of the centrosomal/satellite protein OFD1

The actin motor protein myosin VI is a multivalent protein with diverse functions. Here, we identified and characterised a myosin VI ubiquitous interactor, the oral-facial-digital syndrome 1 (OFD1) protein, whose mutations cause malformations of the face, oral cavity, digits, and polycystic kidney disease. We found that myosin VI regulates the localisation of OFD1 at the centrioles and, as a consequence, the recruitment of the distal appendage protein cep164. Myosin VI depletion in non-tumoural cell lines causes an aberrant localisation of OFD1 along the centriolar walls, which is due to a reduction in the OFD1 mobile fraction. Finally, loss of myosin VI triggers a severe defect in ciliogenesis that could be causally linked to an impairment in the autophagic removal of OFD1 from satellites. Altogether, our results highlight an unprecedent layer of regulation of OFD1 and a pivotal role of myosin VI in coordinating the formation of the distal appendages and primary cilium with important implications for the genetic disorders known as ciliopathies.

H3.3 kinetics predicts chromatin compaction status of parental genomes in early embryos

Background After fertilization, the fusion of gametes results in the formation of totipotent zygote. During sperm-egg fusion, maternal factors participate in parental chromatin remodeling. H3.3 is a histone H3 variant that plays essential roles in mouse embryogenesis. Methods Here, we used transgenic early embryos expressing H3.3-eGFP or H2B-mCherry to elucidate changes of histone mobility. Results We used FRAP analysis to identify that maternally stored H3.3 has a more significant change than H2B during maternal-to-embryonic transition. We also found that H3.3 mobile fraction, which may be regulated by de novo H3.3 incorporation, reflects chromatin compaction of parental genomes in GV oocytes and early embryos. Conclusions Our results show that H3.3 kinetics in GV oocytes and early embryos is highly correlated with chromatin compaction status of parental genomes, indicating critical roles of H3.3 in higher-order chromatin organization.

Dynamics of Bacterial Signal Recognition Particle at a Single Molecule Level

We have studied the localization and dynamics of bacterial Ffh, part of the SRP complex, its receptor FtsY, and of ribosomes in the Gamma-proteobacterium Shewanella putrefaciens. Using structured illumination microscopy, we show that ribosomes show a pronounced accumulation at the cell poles, whereas SRP and FtsY are distributed at distinct sites along the cell membrane, but they are not accumulated at the poles. Single molecule dynamics can be explained by assuming that all three proteins/complexes move as three distinguishable mobility fractions: a low mobility/static fraction may be engaged in translation, medium-fast diffusing fractions may be transition states, and high mobility populations likely represent freely diffusing molecules/complexes. Diffusion constants suggest that SRP and FtsY move together with slow-mobile ribosomes. Inhibition of transcription leads to loss of static molecules and reduction of medium-mobile fractions, in favor of freely diffusing subunits, while inhibition of translation appears to stall the medium mobile fractions. Depletion of FtsY leads to aggregation of Ffh, but not to loss of the medium mobile fraction, indicating that Ffh/SRP can bind to ribosomes independently from FtsY. Heat maps visualizing the three distinct diffusive populations show that while static molecules are mostly clustered at the cell membrane, diffusive molecules are localized throughout the cytosol. The medium fast populations show an intermediate pattern of preferential localization, suggesting that SRP/FtsY/ribosome transition states may form within the cytosol to finally find a translocon.

RUFY3 links Arl8b and JIP4-Dynein complex to regulate lysosome size and positioning

The whole-cell scale spatial organization of lysosomes is regulated by their bidirectional motility on microtubule tracks. Small GTP-binding (G) protein, Arl8b, stimulates the anterograde transport of lysosomes by recruiting adaptor protein SKIP (also known as PLEKHM2), which in turn couples the microtubule motor kinesin-1. Here, we have identified an Arl8b effector, RUN and FYVE domain-containing protein family member 3, RUFY3, which drives the retrograde transport of lysosomes. Artificial targeting of RUFY3 to the surface of mitochondria was sufficient to drive their perinuclear positioning. We find that RUFY3 interacts with the JIP4-Dynein-Dynactin complex and mediates Arl8b association with the retrograde motor complex. The mobile fraction of the total lysosomes per cell was significantly enhanced upon RUFY3 depletion, suggesting that RUFY3 maintains the lysosomes clustering within the perinuclear cloud. Expectedly, RUFY3 knockdown disrupted the perinuclear positioning of lysosomes upon nutrient starvation and/or serum depletion, although lysosome continued to undergo fusion with autophagosomes. Interestingly, lysosome fission events were more frequent in RUFY3-depleted cells and accordingly, there was a striking reduction in lysosome size, an effect that was also observed in dynein and JIP4 depleted cells. These findings indicate that the dynein-dependent “perinuclear cloud” arrangement of lysosomes also regulates the size of these proteolytic compartments and, likely, their cellular roles.

A noncatalytic activity of the H4K20 demethylase DPY-21 regulates condensin DC binding

Condensin is a multi-subunit SMC complex that binds to and compacts chromosomes. Unlike cohesin, in vivo regulators of condensin binding dynamics remain unclear. Here we addressed this question using C. elegans condensin DC, which specifically binds to and represses transcription of both X chromosomes in hermaphrodites for dosage compensation. Mutants of several chromatin modifiers that regulate H4K20me and H4K16ac cause varying degrees of X chromosome derepression. We used fluorescence recovery after photobleaching (FRAP) to analyze how these modifiers regulate condensin DC binding dynamics in vivo. We established FRAP using the SMC4 homolog DPY-27 and showed that a well-characterized ATPase mutation abolishes its binding. The greatest effect on condensin DC dynamics was in a null mutant of the H4K20me2 demethylase DPY-21, where the mobile fraction of the complex reduced from ~30% to 10%. In contrast, a catalytic mutant of dpy-21 did not regulate condensin DC mobility. Separation of catalytic and non-catalytic activity is also supported by Hi-C data in the dpy-21 null mutant. Together, our results indicate that DPY-21 has a non-catalytic role in regulating the dynamics of condensin DC binding, which is important for transcription repression.