Major Rearrangements Research Articles

P1342 Characteristics of the gut microbiota of patients with concomitant inflammatory bowel disease and psoriatic arthritis

Abstract Background Inflammatory bowel disease (IBD) and psoriatic arthritis (PsA) are immune-mediated diseases (IMDs) that have been independently related to shifts in the gut microbiota. In this pilot study, we analyzed whether, in patients in whom both IMIDs coexist, the composition and function of the gut microbiota is different from when only one of the two IMDs exists. Methods Transversal observational study performed at a Spanish tertiary hospital. Ten patients with concomitant IBD and PsA (group A) were included. Two age, gender and disease duration matched control groups were also created, one with IBD-only patients (group B, n=20), and another with PsA-only patients (group C, n=20). Demographic and clinical characteristics were recorded. Stool samples were collected and the variable region V3–V4 of the bacterial 16S rRNA genes present in the feces was PCR-amplified and the resulting amplicons were sequenced on an Illumina NovaSeq 6000 instrument. Short chain fatty acids (SCFA) were analyzed by gas chromatography from the supernatants of the homogenized feces. Dietary assessment was registered by an online food frequency questionnaire specifically designed for intestinal disturbances; foods were transformed into nutrients and dietary compounds. For statistical analysis, ANOVA was used to compare the three groups (when the ANOVA was significant [p<0.05], Bonferroni's test was used for post-hoc comparisons). Results Globally, the microbiota of the different study groups did not show major rearrangements, with alpha diversity not showing statistically significant differences between them. However, beta diversity analyses indicated that the microbiotas of groups C and B were statistically different, with group A occupying an intermediate position. A linear discriminant analysis of the effect size showed that group A was enriched in certain microorganisms such as Akkermansia, while group C was enriched in Bacteroides (Figure 1). The quantification of the fecal levels of SCFA showed no statistical significant differences between the three groups. Moreover, no significant differences were observed regarding energy and nutrient intake between the assessed groups. Conclusion Our results suggest the existence of different gut microbiota profiles in subjects suffering from PsA or IDB, while patients with both conditions have an intermediate composition. These differences do not see to result from different dietary habits, since no differences in nutrient or energy intake between the groups were observed.

Structural insights into binding-site access and ligand recognition by human ABCB1.

ABCB1 is a broad-spectrum efflux pump central to cellular drug handling and multidrug resistance in humans. However, how it is able to recognize and transport a wide range of diverse substrates remains poorly understood. Here we present cryo-EM structures of lipid-embedded human ABCB1 in conformationally distinct apo-, substrate-bound, inhibitor-bound, and nucleotide-trapped states at 3.4-3.9 Å resolution, in the absence of stabilizing antibodies or mutations. The substrate-binding site is located within one half of the molecule and, in the apo state, is obstructed by the transmembrane helix (TM) 4. Substrate and inhibitor binding are distinguished by major TM rearrangements and their ligand binding chemistry, with TM4 playing a central role in all conformational transitions. Furthermore, our data identify secondary structure-breaking residues that impart localized TM flexibility and asymmetry between the two transmembrane domains. The resulting structural changes and lipid interactions that are induced by substrate and inhibitor binding can predict substrate-binding profiles and may direct ABCB1 inhibitor design.

Effect of temperature on circadian clock functioning of trees in the context of global warming.

Plant survival in a warmer world requires the timely adjustment of biological processes to cyclical changes in the new environment. Circadian oscillators have been proposed to contribute to thermal adaptation and plasticity. However, the influence of temperature on circadian clock performance and its impact on plant behaviour in natural ecosystems are not well-understood. We combined bioinformatics, molecular biology and ecophysiology to investigate the effects of increasing temperatures on the functioning of the circadian clock in two closely related tree species from Patagonian forests that constitute examples of adaptation to different thermal environments based on their altitudinal profiles. Nothofagus pumilio, the species from colder environments, showed a major rearrangement of its transcriptome and reduced ability to maintain rhythmicity at high temperatures compared with Nothofagus obliqua, which inhabits warmer zones. In altitude-swap experiments, N. pumilio, but not N. obliqua, showed limited oscillator function in warmer zones of the forest, and reduced survival and growth. Our findings show that interspecific differences in the influence of temperature on circadian clock performance are associated with preferred thermal niches, and to thermal plasticity of seedlings in natural environments, highlighting the potential role of a resonating oscillator in ecological adaptation to a warming environment.

Ancestral genome reconstruction and the evolution of chromosomal rearrangements in Triticeae.

Chromosomal rearrangements (CRs) often cause phenotypic variations. Although several major rearrangements have been identified in Triticeae, a comprehensive study of the order, timing, and breakpoints of CRs has not been conducted. Here, we reconstruct high-quality ancestral genomes for the most recent common ancestor (MRCA) of the Triticeae, and the MRCA of the wheat lineage (Triticum and Aegilops). The protogenes of MRCA of the Triticeae and the wheat lineage are 22,894 and 29,060, respectively, which were arranged in their ancestral order. By partitioning modern Triticeae chromosomes into sets of syntenic regions and linking each to the corresponding protochromosomes, we revisit the rye chromosome structural evolution and propose alternative evolutionary routes. The previously identified 4L/5L reciprocal translocation in rye and Triticum urartu are found to have occurred independently and are unlikely the result of chromosomal introgression following distant hybridization. We also clarify that the 4AL/7BS translocation in tetraploid wheat was a bidirectional rather than unidirectional translocation event. Lastly, we identify several breakpoints in protochromosomes that independently reoccur following Triticeae evolution, representing potential CR hotspots. This study demonstrates that these reconstructed ancestral genomes can serve as special comparative references and facilitate a better understanding of the evolution of structural rearrangements in Triticeae.

Evolution of a novel engineered tripartite viral genome of a torradovirus.

Viruses in the Secoviridae include monopartite and bipartite genomes, suggesting the possibility to study members of this family to experimentally address evolutionary transitions resulting in multipartitism. Torradoviruses are bipartite members of the family Secoviridae characterized by a genus-specific 5' open reading frame, named P21, encoded by RNA2. Here, in a study originally intended to verify if P21 can function in trans, we attempted to provide P21 from a third P21-expressing construct under control of the 35S promoter and containing the 5'- and 3'-untranslated regions (UTRs) of wild-type (WT) RNA2. When this construct was combined with an RNA2 with a complete deletion of the P21 coding region we verified that the P21 provided in trans cannot immediately complement the mutant, but occasional systemic infections in a limited number of the inoculated plants display the presence of a tripartite virus with an actively replicating P21-expressing RNA3. Furthermore, in all the systemically infected plants investigated in six distinct experiments, this replicating RNA3 accumulates deletions in a small region inside the original 3'-UTR provided by the cDNA clone. Such tripartite virus, which we obtained through deconstructing the coding potential of the RNA2 in two distinct RNAs, can be transmitted mechanically and by whiteflies, is competent for virion formation, and its RNA3 is encapsidated. It can be mechanically transferred for 11 serial passages without losing its infectivity or showing major genomic rearrangements. Furthermore, mixing equal amounts of WT and tripartite virus inocula in the same leaf resulted in plants systemically infected only with the WT virus, showing that the tripartite virus has lower fitness than the WT. To our knowledge, this is the first example of an engineered tripartite viral genome becoming stable through artificial evolution in vivo, in plants. This tripartite system was also used to derive a stable viral vector to express green fluorescence protein (GFP) systemically in the context of viral infection.

The timing of large drainage rearrangement in South America: A study based on morphological and ecological evidence

This study aims to characterize and determine the timing of a major drainage rearrangement between two vast river basins, each exceeding 600,000 km2: the Paraná and São Francisco basins in South America. We used geomorphological analyses and the computational Black Top Hat (BTH) method to identify river captures. By using freshwater fish distribution and evolution data, we performer biogeographical analyses to assess the fish dispersal patterns. Our results show that in the past the upper Paraná River (known locally as the Grande River) once flowed into what is now the São Francisco River Basin. Biogeographical analysis corroborates this past connection between Grande and São Fracisco rivers This analysis reveals also that between 6 and 5 and 2 million years ago, a significant drainage rearrangement occurred, when the Paraná River Basin captured the Grande River and its tributary (the Sapucaí River). In this process the São Francisco Basin losing 50,000 km2 of its area to the Paraná River Basin.

A conserved H-bond network in human aquaporin-1 is necessary for native folding and oligomerization

Aquaporins (AQPs) are α-helical transmembrane proteins that conduct water through membranes with high selectivity and permeability. For human AQP1, in addition to the functional Asn-Pro-Ala motifs and the aromatic/Arg selectivity filter within the pore, there are several highly conserved residues that form an expansive hydrogen-bonding network. Previous solid-state nuclear magnetic resonance studies and structural conservation analysis have detailed which residues may be involved in this network. We explored this network by mutating the side chains or backbones involved in hydrogen-bonding, generating the following mutants: N127A, V133P, E142A, T187A, R195A, and S196A. The fold and stability of these mutants were assessed with attenuated total reflection Fourier transform infrared spectroscopy coupled with hydrogen/deuterium exchange upon increasing temperature. We found that replacement of any of the chosen residues to alanine leads to either partial instability or outright misfolding at room temperature, with the latter being most pronounced for the N127A, V133P, T187A, and R195A mutants. Deconvolution analysis of the amide I band revealed considerable secondary structure deviations, with some mutants exhibiting new random coil and β sheet structures. We also found that some of these mutations potentially disrupt the oligomerization of human AQP1. BN-PAGE and DLS data provide evidence toward the loss of tetramers within most of the mutants, meanwhile only the S196A mutant retains tetrameric organization. The molecular dynamics simulation of the wild-type, and the N127A, E142A, and T187A mutants show that these mutations result in major rearrangements of intra- and intermonomer hydrogen-bond networks. Overall, we show that specific point mutations that perturb hydrogen-bonding clusters result in severe misfolding in hAQP1 and disruption of its oligomerization. These data provide valuable insight into the structural stability of human aquaporin-1 and have implications toward other members of the AQP family, as these networks are largely conserved among a variety of human and nonmammalian AQP homologs.

A reference genome for the Harpy Eagle reveals steady demographic decline and chromosomal rearrangements in the origin of Accipitriformes

The Harpy Eagle (Harpia harpyja) is an iconic species that inhabits forested landscapes in Neotropical regions, with decreasing population trends mainly due to habitat loss, and currently classified as vulnerable. Here, we report on a chromosome-scale genome assembly for a female individual combining long reads, optical mapping, and chromatin conformation capture reads. The final assembly spans 1.35 Gb, with N50scaffold equal to 58.1 Mb and BUSCO completeness of 99.7%. We built the first extensive transposable element (TE) library for the Accipitridae to date and identified 7,228 intact TEs. We found a burst of an unknown TE ~ 13–22 million years ago (MYA), coincident with the split of the Harpy Eagle from other Harpiinae eagles. We also report a burst of solo-LTRs and CR1 retrotransposons ~ 31–33 MYA, overlapping with the split of the ancestor to all Harpiinae from other Accipitridae subfamilies. Comparative genomics with other Accipitridae, the closely related Cathartidae and Galloanserae revealed major chromosome-level rearrangements at the basal Accipitriformes genome, in contrast to a conserved ancient genome architecture for the latter two groups. A historical demography reconstruction showed a rapid decline in effective population size over the last 20,000 years. This reference genome serves as a crucial resource for future conservation efforts towards the Harpy Eagle.

Epidermal Differentiation Genes of the Common Wall Lizard Encode Proteins with Extremely Biased Amino Acid Contents.

The epidermal differentiation complex (EDC) is a cluster of genes that code for protein components of cornified cells on the skin surface of amniotes. Squamates are the most species-rich clade of reptiles with skin adaptations to many different environments. As the genetic regulation of the skin epidermis and its evolution has been characterized for only a few species so far, we aimed to determine the organization of the EDC in a model species of squamates, the common wall lizard (Podarcis muralis). By comparative genomics, we identified EDC genes of the wall lizard and compared them with homologs in other amniotes. We found that the EDC of the wall lizard has undergone a major rearrangement leading to a unique order of three ancestral EDC segments. Several subfamilies of EDC genes, such as those encoding epidermal differentiation proteins containing PCCC motifs (EDPCCC) and loricrins, have expanded by gene duplications. Most of the EDPCCC proteins have cysteine contents higher than 50%, whereas glycine constitutes more than 50% of the amino acid residues of loricrin 1. The extremely biased amino acid compositions indicate unique structural properties of these EDC proteins. This study demonstrates that cornification proteins of the common wall lizard differ from homologous proteins of other reptiles, illustrating the evolutionary dynamics of diversifying evolution in squamates.

A suicidal and extensively disordered luciferase with a bright luminescence.

Gaussia luciferase (GLuc) is one of the most luminescent luciferases known and is widely used as a reporter in biochemistry and cell biology. During catalysis, GLuc undergoes inactivation by irreversible covalent modification. The mechanism by which GLuc generates luminescence and how it becomes inactivated are however not known. Here, we show that GLuc unlike other enzymes has an extensively disordered structure with a minimal hydrophobic core and no apparent binding pocket for the main substrate, coelenterazine. From an alanine scan, we identified two Arg residues required for light production. These residues separated with an average of about 22 Å and a major structural rearrangement is required if they are to interact with the substrate simultaneously. We furthermore show that in addition to coelenterazine, GLuc also can oxidize furimazine, however, in this case without production of light. Both substrates result in the formation of adducts with the enzyme, which eventually leads to enzyme inactivation. Our results demonstrate that a rigid protein structure and substrate-binding site are no prerequisites for high enzymatic activity and specificity. In addition to the increased understanding of enzymes in general, the findings will facilitate future improvement of GLuc as a reporter luciferase.

Full prediction of band potentials in semiconductor materials

A machine learning (ML) framework to predict the physical band potentials for a range of semiconductor materials, from metal sulfide, oxide, and nitride, to oxysulfide and oxynitride, is hereby described. A valence band maximum (VBM) model was established via the transfer learning of a large dataset of 2D materials (1382 samples, but with incorrect VBM potentials) onto a much smaller dataset of physically measured VBM for bulk 3D materials (87 samples) on a crystal graph convolutional neural network. This resulted in predictions with experimental accuracy (RMSE = 0.27 eV), which is a 3-fold improvement compared with ML trained on the physical dataset without transfer learning (RMSE = 0.75 eV). When combined with the bandgap prediction model (RMSE = 0.29 eV), a full prediction of conduction and valence band potentials can be made, which to the best of our knowledge, is the first for any ML framework. The variation of band potentials across low-index surfaces was predicted correctly and verified with reported physical potentials. In fact, the framework is able to capture variation in band potentials associated with minor atomic position alterations. Based on this, a general trend between surface atomic displacement and VBM shift was observed across various semiconductor materials. The model is not yet able to cope with major rearrangement of atomic sequence on surface layers, i.e., surface reconstructions, since it was not trained with such data but can be easily done so with specifically designed dataset. As an example application, the ML framework was used for the screening of potential photocatalytic materials for visible light water splitting. A total of 824 materials was successfully identified, including those experimentally-verified in the literature.

A larger TatBC complex associates with TatA clusters for transport of folded proteins across the bacterial cytoplasmic membrane

The twin-arginine translocation (Tat) system transports folded proteins across energized biological membranes in bacteria, plastids, and plant mitochondria. In Escherichia coli, the three membrane proteins TatA, TatB and TatC associate to enable Tat transport. While TatB and TatC together form complexes that bind Tat-dependently transported proteins, the TatA component is responsible for the permeabilization of the membrane during transport. With wild type Tat systems, the TatB- and TatC-containing Tat complexes TC1 and TC2 can be differentiated. Their TatA content has not been resolved, nor could they be assigned to any step of the translocation mechanism. It is therefore a key question of current Tat research to understand how TatA associates with Tat systems during transport. By analyzing affinity-purified Tat complexes with mutations in TatC that selectively enrich either TC1 or TC2, we now for the first time demonstrate that both Tat complexes associate with TatA, but the larger TC2 recruits significantly more TatA than the smaller TC1. Most TatA co-purified as multimeric clusters. Using site-specific photo cross-linking, we could detect TatA–TatC interactions only near TatC transmembrane helices 5 and 6. Substrate-binding did not change the interacting positions but affected the stability of the interaction, pointing to a substrate-induced conformational transition. Together, our findings indicate that TatA clusters associate with TatBC without being integrated into the complex by major rearrangements. The increased TatA affinity of the larger Tat complex TC2 suggests that functional assembly is advanced in this complex.

Genetic determinants of host- and virus-derived insertions for hepatitis E virus replication

Hepatitis E virus (HEV) is a long-neglected RNA virus and the major causative agent of acute viral hepatitis in humans. Recent data suggest that HEV has a very heterogeneous hypervariable region (HVR), which can tolerate major genomic rearrangements. In this study, we identify insertions of previously undescribed sequence snippets in serum samples of a ribavirin treatment failure patient. These insertions increase viral replication while not affecting sensitivity towards ribavirin in a subgenomic replicon assay. All insertions contain a predicted nuclear localization sequence and alanine scanning mutagenesis of lysine residues in the HVR influences viral replication. Sequential replacement of lysine residues additionally alters intracellular localization in a fluorescence dye-coupled construct. Furthermore, distinct sequence patterns outside the HVR are identified as viral determinants that recapitulate the enhancing effect. In conclusion, patient-derived insertions can increase HEV replication and synergistically acting viral determinants in and outside the HVR are described. These results will help to understand the underlying principles of viral adaptation by viral- and host-sequence snatching during the clinical course of infection.

Sustained transmission over two decades of a previously unrecognised MPT64 negative Mycobacterium tuberculosis strain in Queensland, Australia: a whole genome sequencing study

MPT64 is a key protein used for Mycobacterium tuberculosis (MTB) complex strain identification. We describe protracted transmission of an MPT64 negative MTB strain in Queensland, Australia, and explore genomic factors related to its successful spread. All MPT64 negative strains identified between 2002 and 2022 by the Queensland Mycobacteria Reference Laboratory, and an additional 2 isolates from New South Wales (NSW), were whole genome sequenced. Bayesian modelling and phylogeographical analyses were used to assess their evolutionary history and transmission dynamics. Protein structural modelling to understand the putative functional effects of the mutated gene coding for MPT64 protein was performed. Forty-three MPT64 negative isolates were sequenced, belonging to a single MTB cluster of Lineage 4.1.1.1 strains. Combined with a UK dataset of the same lineage, molecular dating estimated 1990 (95% HPD 1987-1993) as the likely time of strain introduction into Australia. Although the strain has spread over a wide geographic area and new cases linked to the cluster continue to arise, phylodynamic analysis suggest the outbreak peaked around 2003. All MPT64 negative strains had a frame shift mutation (delAT, p.Val216fs) within the MPT64 gene, which confers two major structural rearrangements at the C-terminus of the protein. This study uncovered the origins of an MPT64 negative MTB outbreak in Australia, providing a richer understanding of its biology and transmission dynamics, as well as guidance for clinical diagnosis and public health action. The potential spread of MPT64 negative strains undermines the diagnostic utility of the MPT64 immunochromatographic test. This study was funded from an operational budget provided to the Queensland Mycobacterium Reference Laboratory by Pathology Queensland, Queensland Department of Health.

Hairpin protein partitioning from the ER to lipid droplets involves major structural rearrangements.

Lipid droplet (LD) function relies on proteins partitioning between the endoplasmic reticulum (ER) phospholipid bilayer and the LD monolayer membrane to control cellular adaptation to metabolic changes. It has been proposed that these hairpin proteins integrate into both membranes in a similar monotopic topology, enabling their passive lateral diffusion during LD emergence at the ER. Here, we combine biochemical solvent-accessibility assays, electron paramagnetic resonance spectroscopy and intra-molecular crosslinking experiments with molecular dynamics simulations, and determine distinct intramembrane positionings of the ER/LD protein UBXD8 in ER bilayer and LD monolayer membranes. UBXD8 is deeply inserted into the ER bilayer with a V-shaped topology and adopts an open-shallow conformation in the LD monolayer. Major structural rearrangements are required to enable ER-to-LD partitioning. Free energy calculations suggest that such structural transition is unlikely spontaneous, indicating that ER-to-LD protein partitioning relies on more complex mechanisms than anticipated and providing regulatory means for this trans-organelle protein trafficking.

Major chromosome rearrangements in intergeneric wheat × rye hybrids in compatible and incompatible crosses detected by GBS read coverage analysis

The presence of incompatibility alleles in primary amphidiploids constitutes a reproductive barrier in newly synthesized wheat-rye hybrids. To overcome this barrier, the genome stabilization process includes large-scale chromosome rearrangements. In incompatible crosses resulting in fertile amphidiploids, the elimination of one of the incompatible alleles Eml-A1 or Eml-R1b can occur already in the somatic tissue of the wheat × rye hybrid embryo. We observed that the interaction of incompatible loci Eml-A1 of wheat and Eml-R1b of rye after overcoming embryo lethality leads to hybrid sterility in primary triticale. During subsequent seed reproductions (R1, R2 or R3) most of the chromosomes of A, B, D and R subgenomes undergo rearrangement or eliminations to increase the fertility of the amphidiploid by natural selection. Genotyping-by-sequencing (GBS) coverage analysis showed that improved fertility is associated with the elimination of entire and partial chromosomes carrying factors that either cause the disruption of plant development in hybrid plants or lead to the restoration of the euploid number of chromosomes (2n = 56) in the absence of one of the incompatible alleles. Highly fertile offspring obtained in compatible and incompatible crosses can be successfully adapted for the production of triticale pre-breeding stocks.

Uplift and denudation history of the Ellsworth Mountains: insights from low-temperature thermochronology

Abstract. While thermochronological studies have constrained the landscape evolution of several of the crustal blocks of West and East Antarctica, the tectono-thermal evolution of the Ellsworth Mountains remains relatively poorly constrained. These mountains are among the crustal blocks that comprise West Antarctica and exhibit an exceptionally well-preserved Palaeozoic sedimentary sequence. Despite the seminal contribution of Fitzgerald and Stump (1991), who suggested an Early Cretaceous uplift event for the Ellsworth Mountains, further thermochronological studies are required to improve the current understanding of the landscape evolution of this mountain chain. We present new zircon (U–Th) / He (ZHe) ages, which provide insights into the landscape evolution of the Ellsworth Mountains. The ZHe ages collected from near the base and the top of the sequence suggest that these rocks underwent burial reheating after deposition. A cooling event is recorded during the Jurassic–Early Cretaceous, which we interpret as representing exhumation in response to rock uplift of the Ellsworth Mountains. Moreover, our results show that while ZHe ages at the base of the sequence are fully reset, towards the top ZHe ages are partially reset. Uplift and exhumation of the Ellsworth Mountains during the Jurassic–Early Cretaceous was contemporaneous with the rotation and translation of this crustal block with respect to East Antarctica and possibly the Antarctic Peninsula. Furthermore, this period is characterized by widespread extension associated with the disassembly and breakup of Gondwana, with the Ellsworth Mountains playing a key role in the opening of the far southern Atlantic. Based on these results, we suggest that uplift of the Ellsworth Mountains during the disassembly of Gondwana provides additional evidence for major rearrangement of the crustal blocks between the South American, African, Australian and Antarctic plates. Finally, uplift of the Ellsworth Mountains commenced during the Jurassic, which predates the Early Cretaceous uplift of the Transantarctic Mountains. We suggest that the rift-related exhumation of the Ellsworth Mountains occurred throughout two events: (i) a Jurassic uplift associated with the disassembly of southwestern Gondwana and (ii) an Early Cretaceous uplift related with the separation between Antarctica and Australia, which is also recorded in the Transantarctic Mountains.

B-Box transcription factor BBX28 requires CONSTITUTIVE PHOTOMORPHOGENESIS1 to induce shade-avoidance response in Arabidopsis thaliana.

Shade avoidance syndrome is an important adaptive strategy. Under shade, major transcriptional rearrangements underlie the reallocation of resources to elongate vegetative structures and redefine the plant architecture to compete for photosynthesis. BBX28 is a B-box transcription factor involved in seedling de-etiolation and flowering in Arabidopsis (Arabidopsis thaliana), but its function in shade-avoidance response is completely unknown. Here, we studied the function of BBX28 using two mutant and two transgenic lines of Arabidopsis exposed to white light and simulated shade conditions. We found that BBX28 promotes hypocotyl growth under shade through the phytochrome system by perceiving the reduction of red photons but not the reduction of photosynthetically active radiation or blue photons. We demonstrated that hypocotyl growth under shade is sustained by the protein accumulation of BBX28 in the nuclei in a CONSTITUTIVE PHOTOMORPHOGENESIS1 (COP1)-dependent manner at the end of the photoperiod. BBX28 up-regulates the expression of transcription factor- and auxin-related genes, thereby promoting hypocotyl growth under prolonged shade. Overall, our results suggest the role of BBX28 in COP1 signaling to sustain the shade-avoidance response and extend the well-known participation of other members of BBX transcription factors for fine-tuning plant growth under shade.

Structural basis of Integrator-dependent RNA polymerase II termination

The Integrator complex can terminate RNA polymerase II (Pol II) in the promoter-proximal region of genes. Previous work has shed light on how Integrator binds to the paused elongation complex consisting of Pol II, the DRB sensitivity-inducing factor (DSIF) and the negative elongation factor (NELF) and how it cleaves the nascent RNA transcript1, but has not explained how Integrator removes Pol II from the DNA template. Here we present three cryo-electron microscopy structures of the complete Integrator–PP2A complex in different functional states. The structure of the pre-termination complex reveals a previously unresolved, scorpion-tail-shaped INTS10–INTS13–INTS14–INTS15 module that may use its ‘sting’ to open the DSIF DNA clamp and facilitate termination. The structure of the post-termination complex shows that the previously unresolved subunit INTS3 and associated sensor of single-stranded DNA complex (SOSS) factors prevent Pol II rebinding to Integrator after termination. The structure of the free Integrator–PP2A complex in an inactive closed conformation2 reveals that INTS6 blocks the PP2A phosphatase active site. These results lead to a model for how Integrator terminates Pol II transcription in three steps that involve major rearrangements.

Phased Assembly of Neo-Sex Chromosomes Reveals Extensive Y Degeneration and Rapid Genome Evolution in Rumex hastatulus.

Y chromosomes are thought to undergo progressive degeneration due to stepwise loss of recombination and subsequent reduction in selection efficiency. However, the timescales and evolutionary forces driving degeneration remain unclear. To investigate the evolution of sex chromosomes on multiple timescales, we generated a high-quality phased genome assembly of the massive older (<10 MYA) and neo (<200,000 yr) sex chromosomes in the XYY cytotype of the dioecious plant Rumex hastatulus and a hermaphroditic outgroup Rumex salicifolius. Our assemblies, supported by fluorescence in situ hybridization, confirmed that the neo-sex chromosomes were formed by two key events: an X-autosome fusion and a reciprocal translocation between the homologous autosome and the Y chromosome. The enormous sex-linked regions of the X (296 Mb) and two Y chromosomes (503 Mb) both evolved from large repeat-rich genomic regions with low recombination; however, the complete loss of recombination on the Y still led to over 30% gene loss and major rearrangements. In the older sex-linked region, there has been a significant increase in transposable element abundance, even into and near genes. In the neo-sex-linked regions, we observed evidence of extensive rearrangements without gene degeneration and loss. Overall, we inferred significant degeneration during the first 10 million years of Y chromosome evolution but not on very short timescales. Our results indicate that even when sex chromosomes emerge from repetitive regions of already-low recombination, the complete loss of recombination on the Y chromosome still leads to a substantial increase in repetitive element content and gene degeneration.