Modes of Retrotransposition of Long Interspersed Element-1 by Environmental Factors

Approximately 42% of the human genome is composed of endogenous retroelements, and the major retroelement component, long interspersed element-1 (L1), comprises ∼17% of the total genome. A single human cell has more than 5 × 105 copies of L1, 80∼100 copies of which are competent for retrotransposition (RTP). Notably, L1 can induce RTP of other retroelements, such as Alu and SVA, and is believed to function as a driving force of evolution. Although L1-RTP during early embryogenesis has been highlighted in the literature, recent observations revealed that L1-RTP also occurs in somatic cells. However, little is known about how environmental factors induce L1-RTP. Here, we summarize our current understanding of the mechanism of L1-RTP in somatic cells. We have focused on the mode of L1-RTP that is dependent on the basic helix–loop–helix/per–arnt–sim (bHLH/PAS) family of transcription factors. Along with the proposed function of bHLH/PAS proteins in environmental adaptation, we discuss the functional linking of L1-RTP and bHLH/PAS proteins for environmental adaptation and evolution

Unveiling the orbital-selective electronic band reconstruction through the structural phase transition in TaTe2_2

Tantalum ditelluride TaTe$_2$ belongs to the family of layered transition metal dichalcogenides but exhibits a unique structural phase transition at around 170 K that accompanies the rearrangement of the Ta atomic network from a "ribbon chain" to a "butterfly-like" pattern. While multiple mechanisms including Fermi surface nesting and chemical bonding instabilities have been intensively discussed, the origin of this transition remains elusive. Here we investigate the electronic structure of single-crystalline TaTe$_2$ with a particular focus on its modifications through the phase transition, by employing core-level and angle-resolved photoemission spectroscopy combined with first-principles calculations. Temperature-dependent core-level spectroscopy demonstrates a splitting of the Ta $4f$ core-level spectra through the phase transition indicative of the Ta-dominated electronic state reconstruction. Low-energy electronic state measurements further reveal an unusual kink-like band reconstruction occurring at the Brillouin zone boundary, which cannot be explained by Fermi surface nesting or band folding effects. On the basis of the orbital-projected band calculations, this band reconstruction is mainly attributed to the modifications of specific Ta $5d$ states, namely the $d_{XY}$ orbitals (the ones elongating along the ribbon chains) at the center Ta sites of the ribbon chains. The present results highlight the strong orbital-dependent electronic state reconstruction through the phase transition in this system and provide fundamental insights towards understanding complex electron-lattice-bond coupled phenomena.Comment: 21 pages, 5 figure

Binding of 14-3-3β but not 14-3-3σ controls the cytoplasmic localization of CDC25B: Binding site preferences of 14-3-3 subtypes and the subcellular localization of CDC25B

The dual specificity phosphatase CDC25B positively controls the G2-M transition by activating CDK1/cyclin B. The binding of 14-3-3 to CDC25B has been shown to regulate the subcellular redistribution of CDC25B from the nucleus to the cytoplasm and may be correlated with the G2 checkpoint. We used a FLAG-tagged version of CDC25B to study the differences among the binding sites for the 14-3-3 subtypes, 14-3-3β, 14-3-3ε and 14-3-3σ, and the relationship between subtype binding and the subcellular localization of CDC25B. All three subtypes were found to bind to CDC25B. Site-directed mutagenesis studies revealed that 14-3-3β bound exclusively near serine-309 of CDC25B1, which is within a potential consensus motif for 14-3-3 binding. By contrast, 14-3-3σ bound preferentially to a site around serine-216, and the presence of serine-137 and -309 enhanced the binding. In addition to these binding-site differences, we found that the binding of 14-3-3β drove CDC25B to the cytoplasm and that mutation of serine-309 to alanine completely abolished the cytoplasmic localization of CDC25B. However, co-expression of 14-3-3σ and CDC25B did not affect the subeellular localization of CDC25B. Furthermore, serine-309 of CDC25B was sufficient to produce its cytoplasmic distribution with co-expression of 14-3-3β, even when other putative 14-3-3 binding sites were mutated. 14-3-3ε resembled 14-3-3β with regard to its binding to CDC25B and the control of CDC25B subcellujar localization. The results of the present study indicite that two 14-3-3 subtypes can control the subcellular localization of CDC25B by binding to a specific site and that 14-3-3σ has effects on CDC25B other than the control of its subcellular localization

Ultrafast Control of Crystal Structure in a Topological Charge-Density-Wave Material

Optical control of crystal structures is a promising route to change physical properties including topological nature of a targeting material. Time-resolved X-ray diffraction measurements using the X-ray free-electron laser are performed to study the ultrafast lattice dynamics of VTe$_2$, which shows a unique charge-density-wave (CDW) ordering coupled to the topological surface states as a first-order phase transition. A significant oscillation of the CDW amplitude mode is observed at a superlattice reflection as well as Bragg reflections. The frequency of the oscillation is independent of the fluence of the pumping laser, which is prominent to the CDW ordering of the first-order phase transition. Furthermore, the timescale of the photoinduced 1$T^{\prime\prime}$ to 1$T$ phase transition is independent of the period of the CDW amplitude mode

The [4Fe-4S] cluster of sulfurtransferase TtuA desulfurizes TtuB during tRNA modification in Thermus thermophilus

TtuA and TtuB are the sulfurtransferase and sulfur donor proteins, respectively, for biosynthesis of 2-thioribothymidine (s(2)T) at position 54 of transfer RNA (tRNA), which is responsible for adaptation to high temperature environments in Thermus thermophilus. The enzymatic activity of TtuA requires an iron-sulfur (Fe-S) cluster, by which a sulfur atom supplied by TtuB is transferred to the tRNA substrate. Here, we demonstrate that the Fe-S cluster directly receives sulfur from TtuB through its inherent coordination ability. TtuB forms a [4Fe-4S]-TtuB intermediate, but that sulfur is not immediately released from TtuB. Further desulfurization assays and mutation studies demonstrated that the release of sulfur from the thiocarboxylated C-terminus of TtuB is dependent on adenylation of the substrate tRNA, and the essential residue for TtuB desulfurization was identified. Based on these findings, the molecular mechanism of sulfur transfer from TtuB to Fe-S cluster is proposed. Chen et al. demonstrate how the Fe-S cluster receives sulfur from TtuB, a ubiquitin-like sulfur donor during tRNA modification. They find that the release of sulfur from the thiocarboxylated C-terminus of TtuB depends on the adenylation of the substrate tRNA. This study provides molecular insights into the sulfur modification of tRNA

Quick and Spontaneous Transformation between [3Fe–4S] and [4Fe–4S] Iron–Sulfur Clusters in the tRNA-Thiolation Enzyme TtuA

Iron–sulfur (Fe–S) clusters are essential cofactors for enzyme activity. These Fe–S clusters are present in structurally diverse forms, including [4Fe–4S] and [3Fe–4S]. Type-identification of the Fe–S cluster is indispensable in understanding the catalytic mechanism of enzymes. However, identifying [4Fe–4S] and [3Fe–4S] clusters in particular is challenging because of their rapid transformation in response to oxidation–reduction events. In this study, we focused on the relationship between the Fe–S cluster type and the catalytic activity of a tRNA-thiolation enzyme (TtuA). We reconstituted [4Fe–4S]-TtuA, prepared [3Fe–4S]-TtuA by oxidizing [4Fe–4S]-TtuA under strictly anaerobic conditions, and then observed changes in the Fe–S clusters in the samples and the enzymatic activity in the time-course experiments. Electron paramagnetic resonance analysis revealed that [3Fe–4S]-TtuA spontaneously transforms into [4Fe–4S]-TtuA in minutes to one hour without an additional free Fe source in the solution. Although the TtuA immediately after oxidation of [4Fe–4S]-TtuA was inactive [3Fe–4S]-TtuA, its activity recovered to a significant level compared to [4Fe–4S]-TtuA after one hour, corresponding to an increase of [4Fe–4S]-TtuA in the solution. Our findings reveal that [3Fe–4S]-TtuA is highly inactive and unstable. Moreover, time-course analysis of structural changes and activity under strictly anaerobic conditions further unraveled the Fe–S cluster type used by the tRNA-thiolation enzyme