Biology subjects

Kelly, S.

Publications and source records attributed to Kelly, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Diet-microbiome interactions promote enteric nervous system resilience following spinal cord injury

Spinal cord injury (SCI) results in a plethora of physiological dysfunctions across all body systems, including intestinal dysmotility and atrophy of the enteric nervous system (ENS). Typically, the ENS has capacity to recover from perturbation, so it is unclear why intestinal pathophysiologies persist after traumatic spinal injury. With emerging evidence demonstrating SCI-induced alterations to the gut microbiome composition, we hypothesized that modulation of the gut microbiome could contribute to enteric nervous system recovery after injury. Here, we show that intervention with the dietary fiber, inulin prevents ENS atrophy and limits SCI-induced intestinal dysmotility in mice. However, SCI-associated microbiomes and exposure to specific SCI-sensitive gut microbes are not sufficient to modulate injury-induced intestinal dysmotility. Intervention with microbially-derived short-chain fatty acid (SCFA) metabolites prevents ENS dysfunctions and phenocopies inulin treatment in injured mice, implicating these microbiome metabolites in protection of the ENS. Notably, inulin-mediated resilience is dependent on signaling by the cytokine IL-10, highlighting a critical diet-microbiome-immune axis that promotes ENS resilience following SCI. Overall, we demonstrate that diet and microbially-derived signals distinctly impact recovery of the ENS after traumatic spinal injury. This protective diet-microbiome-immune axis may represent a foundation to uncover etiological mechanisms and future therapeutics for SCI-induced neurogenic bowel.

neuroscience↗

bioRxiv2024

Widespread adaptive evolution in the photosystems of angiosperms provides new insight into the evolution of photosystem II repair.

Oxygenic photosynthesis generates the initial energy source which fuels nearly all life on earth. At the heart of the process are the photosystems, pigment binding multi-protein complexes that catalyse the first step of photochemical conversion of light energy into chemical energy. Here, we investigate the molecular evolution at single residue resolution of the plastid-encoded subunits of the photosystems across 773 angiosperm species. We show that despite an extremely high level of conservation, 7% of residues in the photosystems, spanning all photosystem subunits, exhibit hallmarks of adaptive evolution. Through in silico modelling of these adaptive substitutions we uncover the impact of these changes on the properties of the photosystems, focussing on their effects on co-factor binding and the formation of inter-subunit interfaces. We further reveal that evolution has repeatedly destabilised the interaction photosystem II and its D1 subunit, thereby reducing the energetic barrier for D1 turn-over and photosystem repair. Together, these results provide new insight into the trajectory of photosystem evolution during the radiation of the angiosperms.

evolutionary biology↗

bioRxiv2024

Realisation of a key step in the evolution of C4 photosynthesis in rice by genome editing.

C4 photosynthesis is a repeatedly evolved adaptation to photosynthesis that functions to reduce energy loss from photorespiration. The recurrent evolution of this adaptation is achieved through changes in the expression and localisation of several enzymes and transporters that are conventionally used in non-photosynthetic metabolism. These alterations result in the establishment of a biochemical CO2 pump that increases the concentration of CO2 around rubisco in a cellular environment where rubisco is protected from oxygen thus preventing the occurrence of photorespiration. A key step in the evolution of C4 photosynthesis is the change in subcellular localisation of carbonic anhydrase (CA) activity from the mesophyll cell chloroplast to the cytosol, where it catalyzes the first biochemical step of the C4 pathway. Here, we achieve this key step in C4 evolution in the C3 plant Oryza sativa (rice) using genome editing. We show that editing the chloroplast transit peptide of the primary CA isoform in the leaf results in relocalisation of leaf CA activity from the chloroplast to the cytosol. Through analysis of fluorescence induction kinetics in these CA relocalisation lines we uncover a role a new role for chloroplast CA in photosynthetic induction. We also reveal that relocalisation of CA activity to the cytosol causes no detectable perturbation to plant growth or leaf-level CO2 assimilation. Collectively, this work uncovers a novel role for chloroplast CA in C3 plants, and demonstrates that it is possible to achieve a key step in the evolution of C4 photosynthesis by genome editing. Significance statementC4 photosynthesis is a highly efficient adaptation to photosynthesis that fuels the worlds most productive crop plants. It evolved from conventional C3 photosynthesis through a series of changes in leaf biochemistry and anatomy. Here we achieve a key evolutionary step on the path to C4 photosynthesis in rice using genome editing. Specifically, we alter the primary location of carbonic anhydrase activity in the rice leaf from the chloroplast to the cytosol. In doing so, we uncover a novel role for carbonic anhydrase in facilitating the rapid induction kinetics of photosystem II, and initiate a new era of C4 engineering using precision breeding techniques.

plant biology↗

bioRxiv2024

The polyadenosine RNA binding protein Nab2 regulates alternative splicing and intron retention during Drosophila melanogaster brain development

The regulation of cell-specific gene expression patterns requires the coordinated actions of hundreds of proteins, including transcription factors, processing enzymes, and many RNA binding proteins (RBPs). RBPs often become associated with an mRNA immediately after its production and can coordinate processing and quality control steps. Since RBPs can regulate multiple post-transcriptional processing steps, mutations within RBP-encoding genes often lead to pleiotropic effects that alter the physiology of multiple cell types. Thus, identifying how an RBP functions during RNA processing can provide a better understanding of both tissue physiology and mechanisms of disease. In the current study, we investigated how the Drosophila RNA binding protein Nab2, an evolutionary conserved ortholog of human ZC3H14, coordinates mRNA splicing and polyadenylation. ZC3H14 loss in human patients has previously been linked to alterations in nervous system function and disease. Both fly Nab2 and vertebrate ZC3H14 bind to polyadenosine RNA and have been implicated in the control of poly(A) tail length. Here we show that Nab2 loss from developing fly brain tissue also causes widespread changes in alternative splicing and intron retention. Retained introns in Nab2 null larval brains are most often first introns, are surrounded by adenosine-rich sequences, and are often associated with extended poly(A) tails, suggesting that Nab2 coordinates the splicing and polyadenylation of target transcripts. Alterations in splicing patterns ultimately lead to changes in protein abundance in Nab2 null developing brains. Overall, these studies highlight the importance of Nab2 and ZC3H14 in the post-transcriptional regulation of gene expression and provide critical insight into how this family of RBPs coordinates RNA processing during brain development.

genetics↗

bioRxiv2024

Heparan sulphate binding controls in vivo half-life of the HpARI protein family

The parasitic nematode Heligmosomoides polygyrus bakeri secretes the HpARI family, which bind to IL-33, either suppressing (HpARI1 and HpARI2) or enhancing (HpARI3) responses to the cytokine. We previously showed that HpARI2 also bound to DNA via its first Complement Control Protein (CCP1) domain. Here, we find that HpARI1 can also bind DNA, while HpARI3 cannot. Through the production of HpARI2/HpARI3 CCP1 domain-swapped chimeras, DNA-binding ability can be transferred, and correlates with in vivo half-life of administered proteins. We found that HpARI1 and HpARI2 (but not HpARI3) also binds to the extracellular matrix component heparan sulphate (HS), and structural modelling showed a basic charged patch in the CCP1 domain of HpARI1 and HpARI2 (but not HpARI3) which could facilitate these interactions. Finally, a mutant of HpARI2 was produced which lacked DNA and HS binding, and was also shown to have a short half-life in vivo. Therefore, we propose that during infection the suppressive HpARI1 and HpARI2 proteins have long-lasting effects at the site of deposition due to DNA and/or extracellular matrix interactions, while HpARI3 has a shorter half-life due to a lack of these interactions.

immunology↗

bioRxiv2024

Structural basis of nearest-neighbor cooperativity in the ring-shaped gene regulatory protein TRAP from protein engineering and cryo-EM

Homotropic cooperativity is widespread in biological regulation. The homo-oligomeric ring-shaped trp RNA binding attenuation protein (TRAP) from bacillus binds multiple tryptophan ligands (Trp) and becomes activated to bind a specific sequence in the 5 leader region of the trp operon mRNA. Ligand-activated binding to this specific RNA sequence regulates downstream biosynthesis of Trp in a feedback loop. Characterized TRAP variants form 11- or 12-mer rings and bind Trp at the interface between adjacent subunits. Various studies have shown that a pair of loops that gate each Trp binding site is flexible in the absence of the ligand and become ordered upon ligand binding. Thermodynamic measurements of Trp binding have revealed a range of cooperative behavior for different TRAP variants, even if the averaged apparent affinities for Trp have been found to be similar. Proximity between the ligand binding sites, and the ligand-coupled disorder-to-order transition has implicated nearest-neighbor interactions in cooperativity. To establish a solid basis for describing nearest-neighbor cooperativity we engineered dodecameric (12-mer) TRAP variants constructed with two subunits connected by a flexible linker (dTRAP). We mutated one of the protomers such that only every other site was competent for Trp binding. Thermodynamic and structural studies using native mass spectrometry, NMR spectroscopy, and cryo-EM provided unprecedented detail into the thermodynamic and structural basis for the observed ligand binding cooperativity. Such insights can be useful for understanding allosteric control networks and for the development of new ones with defined ligand sensitivity and regulatory control. SignificanceHomo-oligomeric proteins are ubiquitous in biology, and their function is often regulated by activator ligands that bind cooperatively, via poorly understood mechanisms. TRAP is a bacterial protein responsible for sensing changes in cellular tryptophan concentration, and for downregulating its production when levels are elevated. By fusing two subunits via a flexible linker, we assembled protein rings in which every other of its twelve ligand binding sites is incapable of binding. We used calorimetry and native mass spectrometry to measure ligand binding and found that these nearest-neighbor interactions are essential for cooperative ligand binding. Cryo-EM of these engineered proteins provided the means to observe the structure-thermodynamic linkage essential for understanding ligand binding cooperativity.

biophysics↗

bioRxiv2024

Conserved domains and structural motifs that differentiate closely related Rex1 and Rex3 DEDDh Exoribonuclease families are required for their function in yeast

The DEDD family of exonucleases has expanded through evolution whilst retaining a well conserved catalytic domain. One subgroup of DEDD exoribonucleases with very closely related catalytic domain sequences includes the yeast enzymes Rex1 (RNA exonuclease 1) and Rex3, the metazoan REXO1 (RNA exonuclease 1 homologue) and Rexo5 proteins, and the plant protein Sdn5 (small RNA degrading nuclease). Comparison of Alphafold models for these proteins reveals that Rex1, Rexo5 and Sdn5 are structural homologues, consisting of a central catalytic domain inserted within a discontinuous alkaline phosphatase (AlkP) domain. The core AlkP domain of Rex1-related proteins contains distinct surface insertions in different eukaryotic lineages. Yeast Rex1 contains three loops that are modelled to be directed towards the DEDD domain, one of which forms an extended helical arch that is conserved across fungi and plants but absent in metazoan homologues. We show that the arch and an adjacent loop are required for Rex1-mediated processing of 5S rRNA and tRNA in Saccharomyces cerevisiae. Rex3 structural homologues, including REXO1, contain a KIX domain (CREB kinase-inducible domain (KID) interacting domain) and a cysteine- and histidine-rich domain (CHORD) adjacent to a C-terminal DEDD domain. In contrast to Rex1, Rex3 proteins are found in metazoans and fungi but not in plants or algae. Deletion of the KIX domain within yeast Rex3 blocked its function in RNase MRP processing. Taken together, this work identifies evolutionarily conserved structural hallmarks of Rex1 and Rex3 enzymes and demonstrates that these features are required for Rex1- and Rex3-mediated RNA processing pathways in vivo.

molecular biology↗

bioRxiv2024

A prion-like protein regulates the 2-dimensional to 3-dimensional growth transition in the moss Physcomitrium patens

The colonization of the land by plants coincided with the evolution of 3-dimensional (3D) growth; the acquisition of apical cells with the capacity to rotate the plane of cell division. The moss Physcomitrium patens has recently been developed as a model to dissect the genetic basis of 3D growth, an invariable and unifying feature of all land plants. The cytokinin-unresponsive Ppnog1-R mutant incorrectly orients division planes in developing buds and thus fails to make the transition to 3D growth. To reveal the genetic interactors of the PpNOG1 gene, which encodes a protein with a C-terminal UBA domain, we performed a screen and identified the suppressor of nog1a (snog1a) mutant. We have mapped the causative mutation to a gene that encodes a prion-like protein related to FLOE2/3 and demonstrated that the mutant phenotypes observed in both a nog1 disruptant mutant (nog1dis) and snog1a can be attributed to changes in cytokinin perception. We present a revised model for 3D growth and suggest that the 2D-to-3D growth transition is regulated, at least in part, by liquid-liquid phase separation (LLPS). SUMMARY STATEMENTThe transition to 3D growth is negatively regulated by a prion-like protein that both alters cytokinin signaling and has been implicated in liquid-liquid phase separation (LLPS).

plant biology↗

bioRxiv2023

Alternative ergosterol biosynthetic pathways confer antifungal drug resistance in the human pathogens within the Mucor species complex

Mucormycoses are emerging fungal infections caused by a variety of heterogeneous species within the Mucorales order. Among the Mucor species complex, Mucor circinelloides is the most frequently isolated pathogen in mucormycosis patients and despite its clinical significance, there is an absence of established genome manipulation techniques to conduct molecular patho-genesis studies. In this study, we generated a spontaneous uracil auxotrophic strain and developed a genetic transformation procedure to analyze molecular mechanisms conferring antifungal drug resistance. With this new model, phenotypic analyses of gene deletion mutants were conducted to define Erg3 and Erg6a as key biosynthetic enzymes in the M. circinelloides ergosterol pathway. Erg3 is a C-5 sterol desaturase involved in growth, sporulation, virulence, and azole susceptibility. In other fungal pathogens, erg3 mutations confer azole resistance because Erg3 catalyzes the production of a toxic diol upon azole exposure. Surprisingly, M. circinelloides produces only trace amounts of this toxic diol and yet, it is still susceptible to posaconazole and isavuconazole due to alterations in membrane sterol composition. These alterations are severely aggravated by erg3{Delta} mutations, resulting in ergosterol depletion and consequently, hy-persusceptibility to azoles. We also identified Erg6a as the main C-24 sterol methyltransferase, whose activity may be partially rescued by the paralogs Erg6b and Erg6c. Loss of Erg6a function diverts ergosterol synthesis to the production of cholesta-type sterols, resulting in resistance to amphotericin B. Our findings suggest that mutations or epimutations causing loss of Erg6 function may arise during human infections, resulting in antifungal drug resistance to first-line treatments against mucormycoses. ImportanceThe Mucor species complex comprises a variety of opportunistic pathogens known to cause mucormycosis, a potentially lethal fungal infection with limited therapeutic options. The only effective first-line treatments against mucormycosis consist of liposomal formulations of amphotericin B and the triazoles posaconazole and isavuconazole, all of which target components within the ergosterol biosynthetic pathway. This study uncovered M. circinelloides Erg3 and Erg6a as key enzymes to produce ergosterol, a vital constituent of fungal membranes. Absence of any of those enzymes leads to decreased ergosterol and consequently, resistance to ergosterol-binding polyenes such as amphotericin B. Particularly, losing Erg6a function pose a higher threat as the ergosterol pathway is channeled into alternative sterols similar to cholesterol, which maintain membrane permeability. As a result, erg6a mutants survive within the host and disseminate the infection, indicating that Erg6a deficiency may arise during human infections and confer resistance to the most effective treatment against mucormycoses.

microbiology↗

bioRxiv2023

Nitrogen source and Nod factor signaling map out the assemblies of Lotus japonicus root bacterial communities

Symbiosis with soil-dwelling bacteria that fix atmospheric nitrogen allows legume plants to grow in nitrogen-depleted soil. Symbiosis impacts the assembly of root microbiota, but it is not known how this process takes place and whether it is independent of nitrogen nutrition. We use plant and bacterial mutants to address the role of Nod factor signaling on Lotus japonicus root microbiota assembly. We found that Nod factors are produced by symbionts to activate Nod factor signaling in the host, and this modulates the assembly of a symbiotic root microbiota. Lotus plants grown in symbiosis-permissive or suppressive soils delineated three nitrogen-dependent nutritional states: starved, symbiotic, or inorganic. We found that root and rhizosphere microbiomes associated with these states differ in composition and connectivity, demonstrating that symbiosis and inorganic nitrogen impact the legume root microbiota differently. Finally, we demonstrated that selected bacterial genera delineating state-dependent microbiomes have a high level of accurate prediction.

plant biology↗

bioRxiv2023

Long-term survival and induction of operational tolerance to murine islet allografts through the co-transplantation of cyclosporine A eluting microparticles

One strategy to prevent islet rejection, is to create a favorable immune-protective local environment at the transplant site. Herein, we utilize localized cyclosporine A (CsA) delivery to islet grafts via poly(lactic-co-glycolic acid) (PLGA) microparticles to attenuate allograft rejection. CsA microparticles alone significantly delayed islet allograft rejection compared to islets alone (p<0.05). Over 50% (6/11) of recipients receiving CsA microparticles and short-term cytotoxic T lymphocyte-associated antigen 4-Ig (CTLA4-Ig) therapy displayed prolonged allograft survival for 214 days, compared to 25% (2/8) receiving CTLA4-Ig alone (p>0.05). CsA microparticles + CTLA4-Ig islet allografts exhibited reduced T-cell (CD4+ and CD8+ cells) and macrophage (CD68+ cells) infiltration compared to islets alone. We observed reduced mRNA expression of proinflammatory cytokines (IL-6, IL-10, INF-{gamma} & TNF-; p<0.05) and chemokines (CCL2, CCL5, CCL22, and CXCL10; p<0.05) in CsA microparticles + CTLA4-Ig allografts compared to islets alone. Long-term islet allografts contained insulin+ and intra-graft FoxP3+ T regulatory cells. Rapid rejection of third-party skin grafts (C3H) in islet allograft recipients suggested that CsA microparticles + CTLA4-Ig therapy induced donor specific operational tolerance. This study demonstrates that localized CsA drug delivery plus short-course systemic immunosuppression promotes an immune protective transplant niche for allogeneic islets. Article HighlightsO_LISystemic immunosuppression limits patient inclusion for beta cell replacement therapies C_LIO_LILocalized islet graft immunosuppression may reduce drug toxicity and improve graft survival C_LIO_LICyclosporine eluting microparticles + CTLA4-Ig therapy induced donor specific operational tolerance C_LIO_LIGraft localized drug delivery can create an immune protective transplant niche C_LI

immunology↗

bioRxiv2023

Response to Tcherkez and Farquhar: Rubisco adaptation is more limited by phylogenetic constraint than by catalytic trade-off

Rubisco is the primary entry point for carbon into the biosphere. It has been widely proposed that rubisco is highly constrained by catalytic trade-offs due to correlations between the enzymes kinetic traits across species. In previous work, we have shown that these correlations, and thus the strength of catalytic trade-offs, have been over-estimated due to the presence of phylogenetic signal in the kinetic trait data (Bouvier et al., 2021). We demonstrated that only canonical trade-offs between the Michaelis constant for CO2 and carboxylase turnover, and between the Michaelis constants for CO2 and O2 were robust to phylogenetic effects. We further demonstrated that phylogenetic constraints have limited rubisco adaptation to a greater extent than the combined action of catalytic trade-offs. Recently, however, our claims have been contested by Tcherkez and Farquhar (2021), who have argued that the phylogenetic signal we detect in rubisco kinetic traits is an artefact of species sampling, the use of rbcL-based trees for phylogenetic inference, laboratory-to-laboratory variability in kinetic measurements, and homoplasy of the C4 trait. In the present article, we respond to these criticisms on a point-by-point basis and conclusively show that all are either incorrect or invalid. As such, we stand by our original conclusions. Specifically, the magnitude of rubisco catalytic trade-offs have been overestimated in previous analyses due to phylogenetic biases, and rubisco kinetic evolution has in fact been more limited by phylogenetic constraint.

evolutionary biology↗

bioRxiv2023

Genetics of Latin American Diversity (GLAD) Project: insights into population genetics and association studies in recently admixed groups in the Americas

Latin America is underrepresented in genetic studies, which can exacerbate disparities in personalized genomic medicine. However, genetic data of thousands of Latin Americans are already publicly available, but require a bureaucratic maze to navigate all the data access and consenting issues. We present the Genetics of Latin American Diversity (GLAD) Project, a platform that compiles genome-wide information of 54,077 Latin Americans from 39 studies representing 45 geographical regions. Through GLAD, we identified heterogeneous ancestry composition and recent gene-flow across the Americas. Also, we developed a simulated-annealing-based algorithm to match the genetic background of external samples to our database and share summary statistics without transferring individual-level data. Finally, we demonstrate the potential of GLAD as a critical resource for evaluating statistical genetic softwares in the presence of admixture. By making this resource available, we promote genomic research in Latin Americans and contribute to the promises of personalized medicine to more people.

genetics↗

bioRxiv2022

Tudor domain containing protein 5-like (Tdrd5l) identifies a novel germline granule that regulates maternal RNAs

Tudor domain-containing proteins are conserved across the animal kingdom for their function in germline development and fertility. Previously, we demonstrated that Tudor domain-containing protein 5-like (Tdrd5l) plays an important role in the germline where it promotes male identity. However, Tdrd5l is also expressed in both the ovary and testis during later stages of germline development, suggesting that it plays a role in germline differentiation in both sexes. We found that Tdrd5l localizes to a potentially novel germline body and plays a role in post-transcriptional gene regulation. RNA sequencing of Tdrd5l-mutant ovaries compared to wild-type showed that differentially expressed genes were enriched for maternally deposited RNAs. Additionally, embryos laid by Tdrd5l-mutant females exhibited reduced viability and displayed dorsal appendage defects suggesting a failure of proper dorsal-ventral (D/V) patterning. As D/V patterning is dependent on gurken (grk), we examined Grk expression during oogenesis. We observed premature accumulation of Grk protein in nurse cells indicating that translation is no longer properly repressed during mRNA transport to the oocyte. We also observed increased nurse cell accumulation of the cytoplasmic polyadenylation element binding protein Oo18 RNA-Binding Protein (Orb or CPEB), a translational activator of Grk. Decreasing orb function was able to partially rescue the Tdrd5l-mutant phenotype, and so defects in Orb are likely a primary cause of the defects in Tdrd5l mutants. Our data indicate that Tdrd5l is important for translational repression of maternal mRNAs such as orb, and possibly others, following their synthesis in the nurse cells and during their transport to the oocyte.

developmental biology↗

bioRxiv2022

Neurophysiological markers of successful learning in healthy aging

The capacity to learn and memorize is a key determinant for the quality of life, but is known to decline to varying degrees with age. Previous ERP research methods had the limitation that their design did not allow to track the gradual memory formation process. Thus, the neural mechanisms underlying memory formation and the critical features that determine the extent to which aging affects learning are still unknown. By using a visual sequence learning task, which consists of the repeated presentation of a simple sequence of tokens, we are able to track the progress of gradual memory formation through both neurophysiological and behavioral markers. On a neurophysiological level, we focused on two learning related centroparietal ERP components: the P300 and broad positivity. Our results revealed that although both age groups showed significant learning progress, young individuals learned faster and remembered more stimuli than older participants. Successful learning was directly linked to a decrease of P300 amplitude. However, young participants showed larger P300 amplitude with a sharper decrease during the memory formation process. The P300 amplitude predicted learning success in both age groups, was associated with increased fronto-parietal brain network activation and showed good test-retest reliability. Highly, similar results were found for the broad positivity component, which raises the questions if the BP is a distinct component or just a prolonged P300. In a series of analyses, including topographic analysis of variance (TANOVA), equivalence testing and source reconstruction analysis, we addressed the unresolved questions. These analyses revealed concordant distributed brain activation patterns within parietal circuits. Thus, there is no evidence (rather evidence for equivalence) for distinct underlying neural generators for the two components. Taken together, the results highlight the importance of the P300 as a neurophysiological marker of learning and may enable the development of preventive measures for age-related impeded learning.

neuroscience↗

bioRxiv2022

The evolutionary constraints on chloroplast adaptation

The chloroplast (plastid) arose via endosymbiosis of a photosynthetic cyanobacterium by a non-photosynthetic eukaryotic cell approximately 1.5 billion years ago. Although the plastid underwent rapid evolution by genome reduction, its rate of molecular evolution is low and its genome organisation is highly conserved. Here, we investigate the factors that have constrained the rate of molecular evolution of protein coding genes in the plastid genome. Through analysis of 773 angiosperm plastid genomes we show that there is substantial variation in the rate of molecular evolution between genes. We show that variation in the strength of purifying selection between genes is a major determinant of variation in the rate of molecular evolution. We further demonstrate that the distance of a gene from the likely origin of replication influences the rate at which it has evolved, consistent with time and distance dependent mutation gradients. In addition, we show that the amino acid composition of a gene product constraints its substitution tolerance, limiting its rate of molecular evolution. Finally, we demonstrate that the mRNA abundance of a gene is a key factor in determining its rate of molecular evolution, suggesting an interaction between transcription and DNA repair in the plastid. Collectively, we show that the location, composition, and expression of a plastid gene can account for [≥]32% of the variation in its rate of molecular evolution. Thus, these three factors have exerted a substantial limitation on the capacity for adaptive evolution of plastid genes, and constrained the evolvability of the chloroplast.

plant biology↗

bioRxiv2022

Slow molecular evolution of rubisco limits adaptive improvement of CO2 assimilation

Rubisco is the primary entry point for carbon into the biosphere. However, rubisco is widely regarded as inefficient leading many to question whether the enzyme can adapt to become a better catalyst. Through a phylogenetic investigation of the molecular and kinetic evolution of Form I rubisco we demonstrate that rubisco is not stagnant. Instead, we demonstrate rbcL is among the 1% of slowest evolving genes and enzymes on Earth, accumulating one nucleotide substitution every 0.9 million years and one amino acid mutation every 7.2 million years. Despite this, we demonstrate that rubisco catalysis is continuing to evolve toward improved CO2/O2 specificity, carboxylase turnover, and carboxylation efficiency. Consistent with this kinetic adaptation, we reveal that increased rubisco evolution leads to a concomitant improvement in leaf-level CO2 assimilation. Thus, rubisco is continually evolving toward improved catalytic efficiency and CO2 assimilation in plants.

plant biology↗

bioRxiv2022

Evolutionarily conserved effects of Notch signaling drive intestinal graft-versus-host disease in mice and non-human primates

Notch signaling promotes T-cell pathogenicity and graft-versus-host disease (GVHD) after allogeneic hematopoietic cell transplantation (allo-HCT) in mice, with a dominant role for the Delta-like ligand DLL4. To assess if Notchs effects are evolutionarily conserved and identify key mechanisms, we studied antibody-mediated DLL4 blockade in a non-human primate model similar to human allo-HCT. Short-term DLL4 blockade improved post-transplant survival with striking, durable protection from gastrointestinal GVHD, out of proportion to other disease sites. Unlike prior immunosuppressive strategies, anti-DLL4 interfered with a T-cell transcriptional program associated with intestinal infiltration. In cross-species investigations, Notch inhibition decreased surface abundance of the gut-homing integrin a4b7 in conventional T-cells via b1 competition for a4 binding, while preserving a4b7 in regulatory T-cells. Thereby, DLL4/Notch blockade decreased effector T-cell infiltration into the gut, with increased regulatory to conventional T-cell ratios early after allo-HCT. Our results identify a conserved, biologically unique and targetable role of DLL4/Notch signaling in GVHD. One Sentence SummaryNotch signaling promotes pathogenic effector T cell infiltration of the intestine during acute graft-versus-host disease.

immunology↗