bluuebunny/crossref_metadata_2025_split huggingface dataset:
The onset of whole-body regeneration inBotryllus schlosseri: morphological and molecular characterization
Authors: Ricci Lorenzo , Salmon Bastien , Olivier Caroline , Andreoni-Pham Rita , Chaurasia Ankita , Alie Alexandre , Tiozzo Stefano 
Published: January 2022

AbstractColonial tunicates are the only chordates that regularly regenerate a fully functional whole body as part of their asexual life cycle, starting from specific epithelia and/or mesenchymal cells. In addition, in some species, whole-body regeneration (WBR) can also be triggered by extensive injuries, which deplete most of their tissues and organs and leave behind only small fragments of their body.In this manuscript, we characterized the onset of WBR inBotryllus schlosseri,one colonial tunicate long used as a laboratory model. We first analyzed the transcriptomic response to a WBR-triggering injury. Then, through morphological characterization,in vivoobservations via time-lapse, vital dyes, and cell transplant assays, we started to reconstruct the dynamics of the cells triggering regeneration, highlighting an interplay between mesenchymal and epithelial cells. The dynamics described here suggest that WBR inB. schlosseriis initiated by extravascular tissue fragments derived from the injured individuals rather than particular populations of blood-borne cells, as has been described in closely related species. The morphological and molecular datasets here reported provide the background for future mechanistic studies of the WBR ontogenesis inB. schlosseriand allow to compare it with other regenerative processes occurring in other tunicate species and possibly independently evolved.
The AMA1-RON complex drives Plasmodium sporozoite invasion in the mosquito and mammalian hosts
Authors: Fernandes Priyanka , Loubens Manon , Le Borgne Rémi , Marinach Carine , Ardin Beatrice , Briquet Sylvie , Vincensini Laetitia , Hamada Soumia , Hoareau-Coudert Bénédicte , Verbavatz Jean-Marc , Weiner Allon , Silvie Olivier 
Published: January 2022

AbstractPlasmodium sporozoites that are transmitted by blood-feeding female Anopheles mosquitoes invade hepatocytes for an initial round of intracellular replication, leading to the release of merozoites that invade and multiply within red blood cells. Sporozoites and merozoites share a number of proteins that are expressed by both stages, including the Apical Membrane Antigen 1 (AMA1) and the Rhoptry Neck Proteins (RONs). Although AMA1 and RONs are essential for merozoite invasion of erythrocytes during asexual blood stage replication of the parasite, their function in sporozoites is still unclear. Here we show that AMA1 interacts with RONs in mature sporozoites. By using DiCre-mediated conditional gene deletion in P. berghei, we demonstrate that loss of AMA1, RON2 or RON4 in sporozoites impairs colonization of the mosquito salivary glands and invasion of mammalian hepatocytes, without affecting transcellular parasite migration. Our data establish that AMA1 and RONs facilitate host cell invasion across Plasmodium invasive stages, and suggest that sporozoites use the AMA1-RON complex to safely enter the mosquito salivary glands without causing cell damage, to ensure successful parasite transmission. These results open up the possibility of targeting the AMA1-RON complex for transmission-blocking antimalarial strategies.
Caveolae promote successful abscission by controlling intercellular bridge tension during cytokinesis
Authors: Andrade Virginia , Bai Jian , Gupta-Rossi Neetu , Jimenez Ana , Delevoye Cédric , Lamaze Christophe , Echard Arnaud 
Published: January 2022

ABSTRACTDuring cytokinesis, the intercellular bridge (ICB) connecting the daughter cells experiences pulling forces, which delay abscission by preventing the assembly of the ESCRT scission machinery. Abscission is thus triggered by tension release, but how ICB tension is controlled is unknown. Here, we report that caveolae, which are known to control membrane tension upon mechanical stress in interphase cells, are located at the midbody, at the abscission site and at the ICB/cell interface in dividing cells. Functionally, the loss of caveolae delays ESCRT-III recruitment during cytokinesis and impairs abscission. This is the consequence of a 2-fold increase of ICB tension measured by laser ablation, associated with a local increase in myosin II activity at the ICB/cell interface. We thus propose that caveolae buffer membrane tension and limit contractibility at the ICB to promote ESCRT-III assembly and cytokinetic abscission. Altogether, this work reveals an unexpected connection between caveolae and the ESCRT machinery and the first role of caveolae in cell division.TEASERCaveolae limit the tension in the intercellular bridge during cytokinesis to enable ESCRT-III assembly and successful abscission.
Cross-species analysis of LZTR1 loss-of-function mutants demonstrates dependency to RIT1 orthologs
Authors: Cuevas-Navarro Antonio , Rodriguez-Muñoz Laura , Grego-Bessa Joaquim , Cheng Alice , Rauen Katherine A. , Urisman Anatoly , McCormick Frank , Jimenez Gerardo , Castel Pau 
Published: January 2022

AbstractRAS GTPases are highly conserved proteins involved in the regulation of mitogenic signaling. We have previously described a novel Cullin 3 RING E3 ubiquitin ligase complex formed by the substrate adaptor protein LZTR1 that binds, ubiquitinates, and promotes proteasomal degradation of the RAS GTPase RIT1. In addition, others have described that this complex is also responsible for the ubiquitination of canonical RAS GTPases. Here, we have analyzed the phenotypes of LZTR1 loss-of-function mutants in both fruit flies and mice and have demonstrated biochemical dependency on their RIT1 orthologs. Moreover, we show that LZTR1 is haplosufficient in mice and that embryonic lethality of the homozygous null allele can be rescued by deletion of RIT1.
Structure of a bacterial ribonucleoprotein complex central to the control of cell envelope biogenesis
Authors: Islam Md. Saiful , Hardwick Steven W. , Quell Laura , Chirgadze Dimitri Y. , Görke Boris , Luisi Ben F. 
Published: January 2022

AbstractThe biogenesis of the essential precursor of the bacterial cell envelope, glucosamine-6-phosphate (GlcN6P), is controlled through intricate post-transcription networks mediated by GlmZ, a small regulatory RNA (sRNA). GlmZ stimulates translation of the mRNA encoding GlcN6P synthetase in Escherichia coli, but when bound by the protein RapZ, it becomes inactivated through cleavage by the endoribonuclease RNase E. Here we report the cryoEM structure of the RapZ:GlmZ complex, revealing a complementary match of the protein tetrameric quaternary structure to an imperfect structural repeat in the RNA. The RNA is contacted mostly through a highly conserved domain of RapZ that shares deep evolutionary relationship with phosphofructokinase and suggests links between metabolism and riboregulation. We also present the structure of a pre-cleavage encounter intermediate formed between the binary RapZ:GlmZ complex and RNase E that reveals how GlmZ is presented and recognised for cleavage. The structures suggest how other encounter complexes might guide recognition and action of endoribonucleases on target transcripts, and how structured substrates in polycistronic precursors are recognised for processing.
Plant speciation in the Namib Desert: origin of a widespread derivative species from a narrow endemic
Authors: Milton Joseph J. , Affenzeller Matthias , Abbott Richard J. , Comes Hans P. 
Published: January 2022

AbstractBackgroundParapatric (or ‘budding’) speciation is increasingly recognized as an important phenomenon in plant evolution but its role in extreme (e.g. desert) environments is poorly documented.AimsTo test this speciation model in a hypothesized sister pair, the Southwest–North African disjunctSenecio flavusand its putative progenitor, the Namibian Desert endemicS. englerianus.MethodsPhylogenetic inferences were combined with niche divergence tests, morphometrics, and experimental-genetic approaches. We also evaluated the potential role of an African Dry-Corridor (ADC) in promoting the hypothesized northward expansion ofS. flavus(from Namibia), using palaeodistribution models.ResultsBelonging to an isolated (potential ‘relict’) clade, the two morphologically distinct species show pronounced niche divergence in Namibia and signs of digenic-epistatic hybrid incompatibility (based on F2pollen fertility). The presence of ‘connate-fluked’ pappus hairs inS. flavus, likely increasing dispersal ability, is controlled by a single gene locus.ConclusionsOur results provide support for a rare example of ‘budding’ speciation in which awider-ranged derivative (S. flavus) originated at the periphery of asmaller-ranged progenitor (S. englerianus) in the Namib Desert region. The Southwest–North African disjunction ofS. flavuscould have been established by dispersal across intermediate ADC areas during periods of (Late) Pleistocene aridification.
Exploring the onset of B12-based mutualisms using a recently evolved Chlamydomonas auxotroph and B12-producing bacteria
Authors: Bunbury Freddy , Deery Evelyne , Sayer Andrew , Bhardwaj Vaibhav , Harrison Ellen , Warren Martin J. , Smith Alison G. 
Published: January 2022

SummaryCobalamin (vitamin B12), is a cofactor for crucial metabolic reactions in multiple eukaryotic taxa, including major primary producers such as algae, and yet only prokaryotes can produce it. Many bacteria can colonise the algal phycosphere, forming stable communities that gain preferential access to exudates and in return provide compounds, such as B12. Extended coexistence can then drive gene loss, leading to greater algal-bacterial interdependence. In this study, we investigate how a recently evolved B12-dependent strain of Chlamydomonas reinhardtii, metE7, forms a mutualism with certain bacteria, including the rhizobium Mesorhizobium loti and even a strain of the gut bacterium E. coli engineered to produce cobalamin. Although metE7 was supported by B12 producers, its growth in co-culture was slower than the B12-independent wild-type, suggesting that high bacterial B12 provision may be necessary to favour B12 auxotrophs and their evolution. Moreover, we found that an E. coli strain that releases more B12 makes a better mutualistic partner, and although this trait may be more costly in isolation, greater B12 release provided an advantage in co-cultures. We hypothesise that, given the right conditions, bacteria that release more B12 may be selected for, particularly if they form close interactions with B12-dependent algae.Originality-Significance statementMicroalgae are fundamental to the global carbon cycle, and yet despite being photosynthetic they often rely on other organisms for micronutrients. One of these micronutrients is vitamin B12 (cobalamin), which they receive from bacteria. Many environmental studies support the widespread role of B12 in algal-bacterial mutualisms, so here we wished to investigate how these mutualisms may arise evolutionarily by using an experimentally evolved B12-dependent alga and various B12-producers. A B12-producing rhizobium, Mesorhizobium loti, could stably support the B12-dependent Chlamydomonas reinhardtii metE7 strain, and vice versa, but nutrient supplementation increased growth of both species further. metE7 could also be supported by E. coli strains engineered to produce B12, and engineering a strain to release a higher proportion of B12 led to better algal growth, which increased bacterial growth in turn. We suggest that as B12-based mutualisms develop, increased B12 release may be selected for and therefore lead to more productive symbioses.
Control of bacterial immune signaling by a WYL domain transcription factor
Authors: Blankenchip Chelsea L. , Nguyen Justin V. , Lau Rebecca K. , Ye Qiaozhen , Gu Yajie , Corbett Kevin D. 
Published: January 2022

AbstractBacteria use diverse immune systems to defend themselves from ubiquitous viruses termed bacteriophages (phages). Many anti-phage systems function by abortive infection to kill a phage-infected cell, raising the question of how they are regulated to avoid cell killing outside the context of infection. Here, we identify a transcription factor associated with the widespread CBASS bacterial immune system, that we term CapW. CapW forms a homodimer and binds a palindromic DNA sequence in the CBASS promoter region. Two crystal structures of CapW suggest that the protein switches from an unliganded, DNA binding-competent state to a ligand-bound state unable to bind DNA. We show that CapW strongly represses CBASS gene expression in uninfected cells, and that phage infection causes increased CBASS expression in a CapW-dependent manner. Unexpectedly, this CapW-dependent increase in CBASS expression is not required for robust anti-phage activity, suggesting that CapW may mediate CBASS activation and cell death in response to a signal other than phage infection. Our results parallel concurrent reports on the structure and activity of BrxR, a transcription factor associated with the BREX anti-phage system, suggesting that CapW and BrxR are members of a family of universal defense signaling proteins.
Proteomic identification of phosphorylation dependent Septin 7 interactors that drive dendritic spine formation
Authors: Byeon Sujin , Werner Bailey , Falter Reilly , Davidsen Kristian , Snyder Calvin , Ong Shao-En , Yadav Smita 
Published: January 2022

ABSTRACTSeptins are a family of cytoskeletal proteins that regulate several important aspects of neuronal development. Septin 7 (Sept7) is enriched at the base of dendritic spines in excitatory neurons and mediates both spine formation and spine-synapse maturation. Phosphorylation at a conserved C-terminal tail residue of Sept7 mediates its translocation into the dendritic spine head to allow spine-synapse maturation. The mechanistic basis for postsynaptic stability and compartmentalization conferred by phosphorylated Sept7, however, is not known. We report herein the proteomic identification of Sept7 phosphorylation dependent neuronal interactors. Using Sept7 C-terminal phosphopeptide pulldown and biochemical assays, we show that the 14-3-3 family of proteins specifically interact with Sept7 when phosphorylated at the T426 residue. Biochemically, we validate the interaction between Sept7 and 14-3-3 isoform gamma, and show that 14-3-3 gamma is also enriched in mature dendritic spine head. Further, we demonstrate that interaction of phosphorylated Sept7 with 14-3-3 protects it from dephosphorylation, as expression of a 14-3-3 antagonist significantly decreases phosphorylated Sept7 in neurons. This study identifies 14-3-3 proteins as an important physiological regulator of Sept7 function in neuronal development.
SIRT5 is a proviral factor that interacts with SARS-CoV-2 Nsp14 protein
Authors: Walter Marius , Chen Irene P , Vallejo-Gracia Albert , Kim Ik-Jung , Bielska Olga , Lam Victor L , Hayashi Jennifer M , Cruz Andrew , Shah Samah , Gross John D , Krogan Nevan J , Schilling Birgit , Ott Melanie , Verdin Eric 
Published: January 2022

AbstractSARS-CoV-2 non-structural protein Nsp14 is a highly conserved enzyme necessary for viral replication. Nsp14 forms a stable complex with non-structural protein Nsp10 and exhibits exoribonuclease and N7-methyltransferase activities. Protein-interactome studies identified human sirtuin 5 (SIRT5) as a putative binding partner of Nsp14. SIRT5 is an NAD-dependent protein deacylase critical for cellular metabolism that removes succinyl and malonyl groups from lysine residues. Here we investigated the nature of this interaction and the role of SIRT5 during SARS-CoV-2 infection. We showed that SIRT5 stably interacts with Nsp14, but not with Nsp10, suggesting that SIRT5 and Nsp10 are parts of separate complexes. We found that SIRT5 catalytic domain is necessary for the interaction with Nsp14, but that Nsp14 does not appear to be directly deacylated by SIRT5. Furthermore, knock-out of SIRT5 or treatment with specific SIRT5 inhibitors reduced SARS-CoV-2 viral levels in cell-culture experiments. SIRT5 knock-out cells expressed higher basal levels of innate immunity markers and mounted a stronger antiviral response. Our results indicate that SIRT5 is a proviral factor necessary for efficient viral replication, which opens novel avenues for therapeutic interventions.
Single Molecule Analysis of CENP-A Chromatin by High-Speed Atomic Force Microscopy
Authors: Melters Daniël P. , Neuman Keir C. , Rakshit Tatini , Dalal Yamini 
Published: January 2022

AbstractChromatin accessibility is modulated in a variety of ways to create open and closed chromatin states, both of which are critical for eukaryotic gene regulation. At the single molecule level, how accessibility is regulated in the chromatin fiber composed of canonical or variant nucleosomes is a fundamental question in the field. Here, we developed a single-molecule tracking method where we could analyze thousands of canonical H3 and centromeric variant nucleosomes imaged by high-speed atomic force microscopy. This approach allowed us to investigate how changes in nucleosome dynamicsin vitroinform us about chromatin accessibilityin vivo. By high-speed atomic force microscopy, we tracked chromatin dynamics in real time and determined the MSD and diffusion constant for the variant centromeric CENP-A nucleosome. Furthermore, an essential kinetochore protein CENP-C reduces the diffusion constant and mobility of centromeric nucleosomes along the chromatin fiber. We subsequently interrogated how CENP-C modulates CENP-A chromatin dynamicsin vivo. Overexpressing CENP-C resulted in reduced centromeric transcription and impaired loading of new CENP-A molecules. Thus, changes which alter chromatin accessibilityin vitro, also correspondingly alter transcriptionin vivo. These data suggest a model in which variant nucleosomes encode their own diffusion kinetics and mobility, and where binding partners can suppress or enhance mobility.
Rotavirus RNA chaperone mediates global transcriptome-wide increase in RNA backbone flexibility
Authors: Coria Aaztli , Wienecke Anastacia , Borodavka Alexander , Laederach Alain 
Published: January 2022

ABSTRACTDue to genome segmentation, rotaviruses must co-package a set of eleven distinct genomic RNAs. The packaging is mediated by the RNA chaperone NSP2. While the activities of RNA chaperones are well studied with short RNAs, little is known about their global effect on the entire viral transcriptome. Here we used Selective 2′-hydroxyl Acylation Analyzed by Primer Extension and Mutational Profiling (SHAPE-MaP) to systematically examine the secondary structure of the rotavirus transcriptome alone and in the presence of NSP2. Surprisingly, SHAPE-MaP data reveal that despite the well-characterized helix-unwinding activity of NSP2in vitro, its incubation with rotavirus transcripts does not induce a significant change in the SHAPE reactivities. However, a quantitative analysis of the per nucleotide mutation rate, from which SHAPE reactivities are derived, reveals a global five-fold rate increase in the presence of molar excess of NSP2. Further analysis of the mutation rate in the context of structural classification reveals a larger effect on stems rather than loop elements. Together, these data provide the first experimentally derived secondary structure model of the rotavirus transcriptome and reveal that NSP2 exerts a larger effect on stems, while acting by globally increasing RNA backbone flexibility in a protein concentration-dependent manner.
Asymmetric wall ingrowth deposition in Arabidopsis phloem parenchyma transfer cells is tightly associated with sieve elements
Authors: Wei Xiaoyang , Huang Yuan , Collings David A. , McCurdy David W. 
Published: January 2022

AbstractIn Arabidopsis, polarized deposition of wall ingrowths in phloem parenchyma (PP) transfer cells (TCs) occurs adjacent to cells of the sieve element/companion cell (SE/CC) complex. However, the spatial relationships between these different cell types in minor veins, where phloem loading occurs, are poorly understood. PP TC development and wall ingrowth localization were compared to other phloem cells in leaves of Col-0 and the transgenic lines AtSUC2::AtSTP9-GFP and AtSWEET11::AtSWEET11-GFP that identify CCs and PP respectively. The development of PP TCs in minor veins, indicated by deposition of wall ingrowths, proceeded basipetally in leaves. However, not all PP develop ingrowths and higher levels of wall ingrowth deposition occur in abaxial-compared to adaxial-positioned PP TCs. Furthermore, the deposition of wall ingrowths was exclusively initiated on and preferentially covered the PP TC/SE interface, rather than the PP TC/CC interface, and only occurred in PP cells that were adjacent to SEs. Collectively, these results demonstrate the dominant impact of SEs on wall ingrowth deposition in PP TCs and suggest the existence of two sub-types of PP cells in leaf minor veins. Compared to PP cells, PP TCs showed more abundant accumulation of AtSWEET11-GFP, indicating functional differences in phloem loading between PP and PP TCs.HighlightWall ingrowth deposition in phloem parenchyma transfer cells of Arabidopsis leaf minor veins is initiated adjacent to sieve elements, rather than companion cells, and expands to preferentially cover this interface.