A unified view of LCRs across species

Low complexity regions (LCRs) in proteins play a major role in the higher order assemblies of organisms, such as the nucleolus and extracellular matrix. Despite recent focus on how certain features affect the function of LCRs in intracellular higher order assemblies, the relationships between LCRs within proteins, captured by their type and copy number, has yet to be systematically studied. Furthermore, we still lack a unified view of how the sequences, features, relationships and functions of LCRs relate to each other. Here, we developed a systematic and comprehensive approach using dotplot matrices and dimensionality reduction to define LCR relationships proteome-wide and to create a map of LCR sequences capable of integrating any LCR features. As a proof of concept of the importance of LCR relationships, we demonstrate the biological significance of LCR copy number for higher order assembly of the nucleolar protein RPA43 both in vitro and in vivo. Using the LCR map, we revealed the boundaries and connections between regions of sequence space occupied by LCRs, and that LCRs of certain higher order assemblies populated specific regions of sequence space. The integration of LCR relationships and the LCR map provided a unified view of LCRs which uncovered the distribution, distinguishing features, and conserved prevalence of glutamic acid-rich LCRs among nucleolar proteins. When applied across multiple species, this approach highlights how differential occupancy of certain regions of LCR sequence space corresponds to the conservation and emergence of higher order assemblies, such as the plant cell wall or metazoan extracellular matrix. Additionally, we identified previously undescribed regions of LCR sequence space, including a teleost-specific threonine/histidine-rich cluster which exhibits signatures of higher order assemblies. By providing this unified view of LCRs, our approach enables discovery of how LCRs encode higher order assemblies of organisms.

Bubbles and element clusters in rock melts: A chicken and egg problem

<p>The nucleation and growth dynamics of gas bubbles and crystals play a vital function in determining the eruptive behaviour of a magma. Their rate and relative timing, among other factors, are controlled by the magma’s ascent rate. Investigating the kinetics of decompression-induced degassing and crystallization processes can thus give us insight into the rheology of magmas. For example, the rapid decompression of magmas inhibits microlite crystallization and bubble nucleation during ascent leading to crystallization and degassing at shallow levels. This results in a drastic increase in viscosity and an over pressured system, which can lead to violent eruptions. Although many experiments and numerical simulations of magma decompression have been carried out, nascent and initial bubble nucleation remain poorly understood. It is widely accepted that there are two ways bubbles can nucleate within a melt: heterogeneous (on a pre-existing surface) and homogeneous nucleation (within the melt), where homogeneous nucleation requires a higher volatile supersaturation. It has since been tentatively suggested that homogeneous nucleation is simply a variety of heterogeneous nucleation where nucleation occurs on the surface of submicroscopic crystals. However, evidence of these crystals is equivocal. Thus, we have combined novel 2D and 3D structural and chemical microscopy techniques including scanning transmission electron microscopy (STEM), electron energy-loss spectroscopy (EELS) mapping, and atom probe tomography (APT) to investigate the presence of sub-nanometer scale chemical heterogeneities in the vicinity of gas bubbles within an experimental andesitic melt. The combined STEM and EELS data reveal a heterogeneous distribution of bubbles within the melt ranging between 20-100 nm in diameter, some of which have Fe and/or Ca element clusters at the bubble-melt interface. Element clusters enriched in Fe, Ca, and Na are also observed heterogeneously distributed within the melt. The reconstructed APT data reveals bubbles as low ionic density regions overlain by a Na-, Ca-, and K-rich cluster and heterogeneously distributed Fe clusters within the bulk of the melt. Based on these observations, our data demonstrate the existence of nano-scale chemical heterogeneities within the melt and at the bubble-melt interface of bubbles that were previously interpreted to be nucleated homogeneously within the melt, therefore contributing to the proposed hypothesis that homogeneous nucleation could in fact be a variety of heterogeneous nucleation. These results highlight the need to redefine homogeneous nucleation and revisit whether bubbles or crystals occur first within volcanic melts. </p>

Cysteine Borylation in Unprotected Peptides

Synthetic bioconjugation at cysteine (Cys) residues in peptides and proteins has emerged as a powerful tool in chemistry. Soft nucleophilicity of the sulfur in Cys renders an exquisite chemoselectivity with which various functional groups can be placed onto this residue under benign conditions. While a variety of reactions have been successful at producing Cys-based bioconjugates, the majority of these feature sulfur-carbon bonds. We report Cys-borylation, wherein a benchtop stable Pt(II)-based organometallic reagent can be used to transfer a boron-rich cluster onto a sulfur moiety in unprotected peptides forging a boron-sulfur bond. Discovered Cysborylation proceeds at room temperature and is tolerant to a variety of functional groups present in complex polypeptides. The resultant bioconjugates show no additional toxicity compared to their Cys aryl-based congeners. Finally, we demonstrate how the developed Cys-borylation can enhance the proteolytic stability of the produced peptide bioconjugates while maintaining the binding affinity to a protein target.

Cysteine Borylation in Unprotected Peptides

Synthetic bioconjugation at cysteine (Cys) residues in peptides and proteins has emerged as a powerful tool in chemistry. Soft nucleophilicity of the sulfur in Cys renders an exquisite chemoselectivity with which various functional groups can be placed onto this residue under benign conditions. While a variety of reactions have been successful at producing Cys-based bioconjugates, the majority of these feature sulfur-carbon bonds. We report Cys-borylation, wherein a benchtop stable Pt(II)-based organometallic reagent can be used to transfer a boron-rich cluster onto a sulfur moiety in unprotected peptides forging a boron-sulfur bond. Discovered Cysborylation proceeds at room temperature and is tolerant to a variety of functional groups present in complex polypeptides. The resultant bioconjugates show no additional toxicity compared to their Cys aryl-based congeners. Finally, we demonstrate how the developed Cys-borylation can enhance the proteolytic stability of the produced peptide bioconjugates while maintaining the binding affinity to a protein target.

Sequence Composition of Bacterial Chromosome Clones in a Transgressive Root-Knot Nematode Resistance Chromosome Region in Tetraploid Cotton

Plants evolve innate immunity including resistance genes to defend against pest and pathogen attack. Our previous studies in cotton (Gossypium spp.) revealed that one telomeric segment on chromosome (Chr) 11 in G. hirsutum cv. Acala NemX (rkn1 locus) contributed to transgressive resistance to the plant parasitic nematode Meloidogyne incognita, but the highly homologous segment on homoeologous Chr 21 had no resistance contribution. To better understand the resistance mechanism, a bacterial chromosome (BAC) library of Acala N901 (Acala NemX resistance source) was used to select, sequence, and analyze BAC clones associated with SSR markers in the complex rkn1 resistance region. Sequence alignment with the susceptible G. hirsutum cv. TM-1 genome indicated that 23 BACs mapped to TM-1-Chr11 and 18 BACs mapped to TM-1-Chr 21. Genetic and physical mapping confirmed less BAC sequence (53–84%) mapped with the TM-1 genome in the rkn1 region on Chr 11 than to the homologous region (>89%) on Chr 21. A 3.1-cM genetic distance between the rkn1 flanking markers CIR316 and CIR069 was mapped in a Pima S-7 × Acala NemX RIL population with a physical distance ∼1 Mbp in TM-1. NCBI Blast and Gene annotation indicated that both Chr 11 and Chr 21 harbor resistance gene-rich cluster regions, but more multiple homologous copies of Resistance (R) proteins and of adjacent transposable elements (TE) are present within Chr 11 than within Chr 21. (CC)-NB-LRR type R proteins were found in the rkn1 region close to CIR316, and (TIR)-NB-LRR type R proteins were identified in another resistance rich region 10 cM from CIR 316 (∼3.1 Mbp in the TM-1 genome). The identified unique insertion/deletion in NB-ARC domain, different copies of LRR domain, multiple copies or duplication of R proteins, adjacent protein kinases, or TE in the rkn1 region on Chr 11 might be major factors contributing to complex recombination and transgressive resistance.

The effects of rotation on the lithium depletion of G- and K-dwarfs in Messier 35

ABSTRACT New fibre spectroscopy and radial velocities from the WIYN telescope are used to measure photospheric lithium in 242 high-probability, zero-age main-sequence F- to K-type members of the rich cluster M35. Combining these with published rotation periods, the connection between lithium depletion and rotation is studied in unprecedented detail. At Teff < 5500 K there is a strong relationship between faster rotation and less Li depletion, although with a dispersion larger than measurement uncertainties. Components of photometrically identified binary systems follow the same relationship. A correlation is also established between faster rotation rate (or smaller Rossby number), decreased Li depletion and larger stellar radius at a given Teff. These results support models where star-spots and interior magnetic fields lead to inflated radii and reduced Li depletion during the pre-main-sequence (PMS) phase for the fastest rotators. However, the data are also consistent with the idea that all stars suffered lower levels of Li depletion than predicted by standard PMS models, perhaps because of deficiencies in those models or because saturated levels of magnetic activity suppress Li depletion equally in PMS stars of similar Teff regardless of rotation rate, and that slower rotators subsequently experience more mixing and post-PMS Li depletion.

GASP

We present atomic hydrogen (H I) observations with the Jansky Very Large Array of one of the jellyfish galaxies in the GAs Stripping Phenomena sample, JO201. This massive galaxy (M* = 3.5 × 1010 M⊙) is falling along the line-of-sight towards the centre of a rich cluster (M200 ∼ 1.6 × 1015 M⊙, σcl ∼ 982 ± 55 km s−1) at a high velocity ≥3363 km s−1. Its Hα emission shows a ∼40 kpc tail, which is closely confined to its stellar disc and a ∼100 kpc tail extending further out. We find that H I emission only coincides with the shorter clumpy Hα tail, while no H I emission is detected along the ∼100 kpc Hα tail. In total, we measured an H I mass of MHI = 1.65 × 109 M⊙, which is about 60% lower than expected based on its stellar mass and stellar surface density. We compared JO201 to another jellyfish in the GASP sample, JO206 (of a similar mass but living in a ten times less massive cluster), and we find that they are similarly H I-deficient. Of the total H I mass in JO201, about 30% lies outside the galaxy disc in projection. This H I fraction is probably a lower limit since the velocity distribution shows that most of the H I is redshifted relative to the stellar disc and could be outside the disc. The global star formation rate (SFR) analysis of JO201 suggests an enhanced star formation for its observed H I content. The observed SFR would be expected if JO201 had ten times its current H I mass. The disc is the main contributor of the high star formation efficiency at a given H I gas density for both galaxies, but their tails also show higher star formation efficiencies compared to the outer regions of field galaxies. Generally, we find that JO201 and JO206 are similar based on their H I content, stellar mass, and star formation rate. This finding is unexpected considering their different environments. A toy model comparing the ram pressure of the intracluster medium (ICM) versus the restoring forces of these galaxies suggests that the ram pressure strength exerted on them could be comparable if we consider their 3D orbital velocities and radial distances relative to the clusters.

Nuclear accumulation of ZFP36L1 is cell cycle-dependent and determined by a C-terminal serine-rich cluster

ZFP36L1 is an RNA-binding protein responsible for mRNA decay in the cytoplasm. ZFP36L1 has also been suggested as a nuclear-cytoplasmic shuttling protein because it contains a potential nuclear localization signal and a nuclear export signal. However, it remains unclear how the nuclear localization of ZFP36L1 is controlled. In this study, we provide evidence that the nuclear accumulation of ZFP36L1 protein is modulated in a cell cycle-dependent manner. ZFP36L1 protein accumulation in fractionated nuclei was particularly prominent in cells arrested at G1-/S-phase boundary, while it was downregulated in S-phase cells, and eventually disappeared in G2-phase nuclei. Moreover, forced nuclear targeting of ZFP36L1 revealed marked downregulation of this protein in S- and G2-phase cells, suggesting that ZFP36L1 can be eliminated in the nucleus. The C-terminal serine-rich cluster of ZFP36L1 is critical for the regulation of its nuclear accumulation because truncation of this probable disordered region enhanced the nuclear localization of ZFP36L1, increased its stability and abolished its cell cycle-dependent fluctuations. These findings provide the first hints to the question of how ZFP36L1 nuclear accumulation is controlled during the course of the cell cycle.