Biology subjects

Ferguson, B. J.

Publications and source records attributed to Ferguson, B. J..

At least 19 recordsLinked to original sources

bioRxiv2026

VigExp: A functionally verified platform for aiding cowpea (Vigna unguiculata) and related legume crop improvement

Legumes include some of the worlds most significant crop species, such as cowpea (Vigna unguiculata), a subsistence crop widely grown in sub-Saharan Africa. Despite their importance, legume crop improvement is hindered by a lack of high-resolution expression data, particularly for reproductive tissues and cell types. Here, we report on VigExp, a tool for visualising cowpea gene expression datasets. We demonstrate its utility across a range of vegetative and reproductive cell types of varieties IT97K-499-35 and IT86D-1010, which exhibit 93.75% protein sequence conservation and are amenable to stable transformation. This includes previously published transcriptomes of vegetative, floral and seed tissues, combined with developmentally staged male and female reproductive tissues. Also integrated are novel transcriptomes of laser-captured cell types covering reproductive development from meiosis to early embryo formation post-fertilisation. Spatial expression patterns and transcript levels can be visualised through an electronic fluorescent pictograph (eFP) browser. Validated by RT-qPCR, in situ hybridisation, transgenic, and CRISPR gene editing analyses, the predictive accuracy of VigExp matches prior cowpea functional study observations. Critical genes for nodule development and regulation were also identified and their expression patterns established in cowpea. Novel reference genes, constitutively expressed gene promoters for visualisation markers/gene-editing, and tissue- and cell-specific gene promoters for targeting these regions, were identified. The A-type cyclin, VuTAM2, was also identified, with a critical role in male meiosis established. Collectively, VigExp represents an adaptable and updatable resource to support crop improvement in cowpea and other legumes, which are often highly syntenic with respect to genome composition.

plant biology↗

bioRxiv2025

Comparative Dual RNA-Seq Analysis of Eight Orientia tsutsugamushi Strains in Endothelial Cells Reveals Regulatory Patterns in Bacterial and Host Pathways During Infection

Orientia tsutsugamushi is an obligate intracellular bacterium that causes the mite-borne human disease scrub typhus. The species is characterised by having many strains that differ in their ability to cause disease in murine infection models and in human patients. The genomes of a diverse set of Orientia tsutsugamushi strains have recently been analysed in detail, revealing broadly similar gene content with genomes differing primarily in synteny and in the composition of a large arsenal of predicted secreted effector proteins. Given the similarity in gene content, here we asked whether the observed differences in virulence were driven by genome-wide differences in gene expression of bacterial genes, and differences in the ensuing response of infected host cells. To explore this, we carried out a dual RNA sequencing analysis of eight diverse strains of Orientia tsutsugamushi grown in cultured human endothelial cells. An overall analysis found no clear patterns in the bacterial or host gene expression patterns that correlate with the ability to cause disease. We found that all strains induce a strong type 1 interferon response in endothelial cells, but that within that broad response each strain has a unique fingerprint of induced genes likely leading to different disease outcomes when combined with a complex immune system in vivo. We compared expression levels of orthologous genes between different strains and identified some bacterial pathways with constant expression levels whilst others were more variable, leading to the identification of specific pathways under tight transcriptional control during cellular infection. Together our data show that inter-strain differences in virulence are not defined by expression levels of any one set of bacterial or host genes and also reveal insights into transcriptional regulation of different pathways in Orientia tsutsugamushi.

microbiology↗

bioRxiv2025

The biofuel producing legume tree, Pongamia pinnata, offers strong potential for carbon sequestration

Pongamia pinnata (Linn.) Pierre, also called Millittia pinnata or Indian beach, is a fast-growing legume tree that has gained considerable attention for its potential as a feedstock for biofuel. In this study, we assessed the growth characteristics and carbon sequestering potential of Pongamia grown under sub-tropical environments. At two different sites located in Queensland, Australia, Pongamia was found to produce considerable biomass, even when planted in nutrient-poor environments having low soil organic carbon. The seedlings planted were all derived directly from genetically diverse, yet related seed. Variability observed in growth appeared to be associated with the mother tree from which the seeds were sourced, underscoring the importance of planting elite genetic material for commercial purposes. Pongamia is known to be drought tolerant, with findings here demonstrating that even young seedlings have this characteristic. Collectively, our findings indicate that Pongamia can grow quickly, reaching a biomass of 13-19 kg over 3-4 years in our studies, and sequester high quantities of carbon, at 2.9 to 4.0 t of carbon per ha (assuming a tree density of [~]450/ha), even when planted in suboptimal growing conditions on marginal, nutrient-poor lands.

plant biology↗

bioRxiv2025

Codon Usage Bias Analysis of the WRKY Gene Family in Musa acuminata

Codon usage bias (CUB) is a universal phenomenon across all organisms and species, providing valuable insights into codon usage patterns to understand evolutionary mechanisms. The WRKY transcription factor family plays a pivotal role in regulating plant responses to various stresses at both physiological and biochemical levels. Bananas (Musa spp.), widely consumed as a fruit or staple food, are an important horticulture crop in the tropical and subtropical regions around the world. A total of 151 WRKY transcription factors were identified across the genome of the Musa acuminata banana cultivar Guijiao 9, which has been shown to be resistant to the Tropical Race 4 of the Fusarium wilt of banana. The codons of these transcription factors, selected based on their expression from RNA-Seq data, were analysed to investigate the evolutionary patterns of WRKY genes in Musa acuminata. The average GC content of MaWRKY genes was 55.49%, with a GC3 content of 62.13%, indicating a preference for G/C-ending codons. Among the codons, 27 were identified as high frequency, with 22 ending in G or C. The high effective number of codons (ENC) values (34.53-60.79) and low codon adaptation index (CAI) values (0.143-0.3) suggested weak CUB and that was associated with low gene expression levels. ENC-plot, PR2-plot, and neutrality analysis revealed that both natural selection and mutation pressure contributed to the observed CUB, with natural selection being the dominant factor influencing the codon usage of MaWRKY genes in M. acuminata Guijiao 9. Fourteen optimal codons, all ending in G or C, were identified. This analysis provides a theoretical foundation for further understanding the evolutionary mechanisms of WRKY genes and identifying key genes involved in resistance to biotic stress in Musa. Analysing the evolution of WRKY family genes can offer valuable genetic insights into banana growth and development, supporting the phenotypic selection of banana hybrids in breeding programs.

plant biology↗

bioRxiv2024

Targeting DNA-PK is a highly conserved poxvirus innate immune evasion mechanism

The sensing of viral nucleic acid by pattern recognition receptors (PRRs) is essential for initiation of a type-I interferon response against infection. Intracellular DNA sensing PRRs are responsible for initiating innate immune responses to poxviruses and other double-stranded DNA viruses. Poxviruses, in turn, encode an armoury of immunomodulators that inhibit this host defence mechanism. DNA-dependent protein kinase (DNA-PK) is an essential component of the cGAS/STING-dependent viral DNA sensing machinery that leads to the initiation of a type-I interferon response during poxvirus infection. Poxviruses counter this host sensing mechanism using the C4/C10 family of proteins that target DNA-PK, interfering with its ability to bind viral DNA. Although the DNA-PK complex, known also for its role in double strand break repair, is conserved across multiple taxa, its function in innate immunity outside mammals is unexplored. Here we analysed the contribution of DNA-PK to poxvirus DNA sensing in chickens, a species that is evolutionarily distant from mammals, but that is also infected by poxviruses. We found that DNA-PK functions as a DNA sensor in chickens, and this process is countered by C4/C10 family members found in fowlpox virus. This host/pathogen interaction is conserved across a broader range of species than other mechanisms of poxvirus antagonism of innate immune sensing, which may reflect the difficulty of the host in evolving escape mechanisms that interfere with a protein that is essential for maintenance of genomic stability.

immunology↗

bioRxiv2024

Molecular basis of autoimmune disease protection by MDA5 variants

MDA5 recognizes dsRNA from viruses and retroelements. Cooperative filament formation and ATP-dependent proofreading confer MDA5 with the necessary sensitivity and specificity for dsRNA. The gene encoding MDA5 is a hotspot for disease-associated variants. Many MDA5 variants are associated with protection from autoimmune disease, while increasing the risk of infection and chronic inflammation, but how these variants affect MDA5-dependent RNA sensing remains unclear. Here, we determine the consequences of autoimmune-protective MDA5 variants on the molecular structure and activities of MDA5. The rare variants E627* and I923V reduce the cellular interferon response to picornavirus infection and are deficient in filament formation. The I923V variant is ATPase hyperactive, causing premature dissociation from dsRNA. Cryo-EM structures of MDA5 I923V bound to dsRNA at different stages of ATP hydrolysis reveal smaller RNA binding interfaces, leading to excessive proofreading activity. Variants R843H and T946A, which are genetically linked and cause mild phenotypes, have no effect on dsRNA recognition, suggesting an indirect disease mechanism. We conclude that the autoimmune-protective MDA5 variants lead to a loss of MDA5-dependent signaling via multiple distinct mechanisms.

biochemistry↗

bioRxiv2024

New integrative vectors increase Agrobacterium rhizogenes transformation and help characterise roles for soybean GmTML gene family members

Hairy-root transformation is widely used to generate transgenic plant roots for genetic functional characterisation studies. However, transformation efficiency can be limited, largely due to the use of binary vectors. Here, we report on the development of novel integrative vectors that significantly increase the transformation efficiency of hairy roots. This includes pHGUS7, for promoter::reporter visualisation studies, and pHOG13, for genetic insertion and overexpression studies. These vectors have been designed to simplify cloning workflows, enhance the selection of positively transformed Agrobacterium colonies, and increase the transformation efficiency and ease of selection of genetically modified hairy roots. To demonstrate the efficacy of the new vectors, Too Much Love (TML) encoding genes acting in the Autoregulation Of Nodulation (AON) pathway of soybean were investigated. Both constructs provided significantly higher transformation rates than the binary vector control, often resulting in >70% of the roots being transformed. Overexpression of each individual TML encoding gene (GmTML1a, GmTML1b and GmTML2) using pHOG13 resulted in a significant reduction in nodule number, demonstrating the role of all three in inhibiting nodule organogenesis. Moreover, reporter-fusions with the promoter of each TML encoding gene using pHGUS7 revealed that each exhibits a unique pattern of expression in nodules, with GmTML1b displaying considerably stronger expression than GmTML1a or GmTML2. Taken together, these results demonstrate the utility and efficiency of the new pHOG13 and pHGUS7 integrative vectors in hairy-root transformation, and improve our understanding of the critical TML-encoding genes in soybean nodulation control.

plant biology↗

bioRxiv2024

Modelling molecular differences in the innate immune system responses of chickens and ducks to highly pathogenic avian influenza virus

Highly pathogenic avian influenza virus (HPAIV) presents a global threat to chicken livestock; chickens infected by HPAIV tend to show severe symptoms and high mortality rates. In 2022, the largest recorded outbreak of HPAIV in Europe resulted in millions of chickens being culled in the UK alone to try to prevent further spread. Unlike chickens, mallard ducks show reduced symptom severity and lower mortality rates to HPAIV infection. Research into the immune system responses of these two species shows they differ in their molecular outputs: chickens produce a pro-inflammatory response; mallards produce an anti-viral response. These differences in immune responses are thought to be in part due to chickens missing pattern recognition receptor retinoic acid-inducible gene-I (RIG-I). This project aimed to model the innate immune systems of chickens and mallard ducks to an abstracted molecular level. A literature search was conducted, and the immune systems were modelled in NetLogo as an avian innate immune response agent-based model (AIIRABM). The AIIRABM enabled examination of the relative importance of molecular differences between the chicken and mallard duck innate immune systems and produced similar differences in chicken and mallard duck molecular outputs to those observed in vitro and in vivo. Simulation experiments with the AIIRABM supported the molecular difference RIG-I as key in causing the differences in the chicken and mallard duck innate immune responses to HPAIV. The AIIRABM will be used in further research on the chicken and mallard duck immune responses to HPAIV as the baseline in an iterative modelling cycle.

immunology↗

bioRxiv2023

Mechanisms of type I interferon production by chicken TLR21

The innate immune response relies on the ability of host cells to rapidly detect and respond to microbial nucleic acids. Toll-like receptors (TLRs), a class of pattern recognition receptors (PRRs), play a fundamental role in distinguishing self from non-self at the molecular level. In this study, we focused on TLR21, an avian TLR that recognizes DNA motifs commonly found in bacterial genomic DNA, specifically unmethylated CpG motifs. TLR21 is believed to act as a functional homologue to mammalian TLR9. By analysing TLR21 signalling in chickens, we sought to elucidate avian TLR21 activation outputs in parallel to that of other nucleic acid species. Our analyses revealed that chicken TLR21 (chTLR21) triggers the activation of NF-{kappa}B and induces a potent type-I interferon response in chicken macrophages, similar to the signalling cascades observed in mammalian TLR9 activation. Notably, the transcription of interferon beta (IFNB) by chTLR21 was found to be dependent on both NF-{kappa}B and IRF7 signalling, but independent of the TBK1 kinase, a distinctive feature of mammalian TLR9 signalling. These findings highlight the conservation of critical signalling components and downstream responses between avian TLR21 and mammalian TLR9, despite their divergent evolutionary origins. These insights into the evolutionarily conserved mechanisms of nucleic acid sensing contribute to the broader understanding of host-pathogen interactions across species.

immunology↗

bioRxiv2023

Contrasting functions of ATP hydrolysis by MDA5 and LGP2 in viral RNA sensing

Cytosolic long double-stranded RNA (dsRNA), among the most potent proinflammatory signals, is recognized by MDA5. MDA5 binds dsRNA cooperatively, forming helical filaments. ATP hydrolysis by MDA5 fulfills a proofreading function by promoting dissociation of shorter endogenous dsRNAs from MDA5 while allowing longer viral dsRNAs to remain bound leading to activation of interferon-{beta} responses. Here, we show that adjacent MDA5 subunits in MDA5-dsRNA filaments hydrolyze ATP cooperatively, inducing cooperative filament disassembly. This amplifies the RNA footprint expansion that accompanies each round of ATP hydrolysis and allows MDA5 to displace tightly bound proteins from dsRNA. Our electron microscopy and biochemical assays show that LGP2 binds to dsRNA at internal binding sites through noncooperative ATP hydrolysis. Unlike MDA5, LGP2 has low nucleic acid selectivity and can hydrolyze GTP and CTP as well as ATP. Binding of LGP2 to dsRNA promotes nucleation of MDA5 filament assembly resulting in shorter filaments. Molecular modeling of the MDA5-LGP2 interface suggests that MDA5 interacts with dsRNA stem-bound rather than end-bound LGP2. We conclude that NTPase-dependent binding of LGP2 to internal sites on dsRNA increases the number and signaling output of MDA5-dsRNA complexes. Our work identifies novel molecular mechanisms contributing the selectivity and sensitivity of cytosolic dsRNA sensing. KEY POINTSO_LICooperative ATP hydrolysis in MDA5 filaments confers selectivity for dsRNA and displaces other proteins from RNA C_LIO_LINoncooperative NTP hydrolysis by LGP2 induces binding to internal RNA sites with low selectivity C_LIO_LIRNA stem-bound LGP2 nucleates assembly of MDA5 signaling complexes on a broader set of RNA ligands C_LI

biochemistry↗

bioRxiv2022

Transcriptional reprogramming of natural killer cells by vaccinia virus shows both distinct and conserved features with mCMV

Natural killer (NK) cells have an established role in controlling poxvirus infection and there is a growing interest to exploit their capabilities in the context of poxvirus-based oncolytic therapy and vaccination. How NK cells recognise poxvirus-infected cells to become activated remains unclear. To address this knowledge gap, we studied the NK cell response to vaccinia virus (VACV) in vivo, using a systemic infection murine model. We found broad alterations in NK cells transcriptional activity in VACV-infected mice, consistent with both direct target cell recognition and cytokine exposure. There were also alterations in the expression levels of specific NK surface receptors (NKRs), including the Ly49 family and SLAM receptors, as well as upregulation of memory-associated NK markers. Despite the latter observation, adoptive transfer of NK memory populations did not confer protection from re-infection. Comparison with the NK cell response to murine cytomegalovirus (MCMV) infection highlighted common features, but also distinct NK transcriptional programmes initiated by VACV. Finally, there was a clear overlap between the NK transcriptional response in humans vaccinated with an attenuated VACV, modified vaccinia Ankara (MVA), demonstrating conservation between the NK response in these different host species. Overall, this study provides new data about NK cell activation, function, and homeostasis during VACV infection, and may have implication for the design of VACV-based therapeutics.

immunology↗

bioRxiv2022

DNA-PKcs is required for cGAS/STING-dependent viral DNA sensing in human cells

To mount an efficient interferon response to virus infection, intracellular pattern recognition receptors (PRRs) sense viral nucleic acids and activate anti-viral gene transcription. The mechanisms by which intracellular DNA and DNA viruses are sensed are relevant not only to antiviral innate immunity, but also to autoinflammation and anti-tumour immunity through initiation of sterile inflammation by self-DNA recognition. The PRRs that directly sense and respond to viral or damaged self-DNA function by signalling to activate interferon regulatory factor (IRF)-dependent type one interferon (IFN-I) transcription. We and others have previously defined DNA-dependent protein kinase (DNA-PK) as an essential component of the DNA-dependent antiviral innate immune system. Here, we show that DNA-PK is essential for STING-dependent IFN-I responses in human cells during stimulation with exogenous DNA and infection with DNA viruses.

immunology↗

bioRxiv2022

LUBAC is required for RIG-I sensing of RNA viruses

The ability of cells to mount an interferon response to virus infections depends on intracellular nucleic acid sensing pattern recognition receptors (PRRs). RIG-I is an intracellular PRR that binds short double stranded viral RNAs to trigger MAVS-dependent signalling. The RIG-I/MAVS signalling complex requires the coordinated activity of multiple kinases and E3 ubiquitin ligases to activate the transcription factors that drive type I and type III interferon production from infected cells. The linear ubiquitin chain assembly complex (LUBAC) regulates the activity of multiple receptor signalling pathways in both ligase-dependent and -independent ways. Here, we show that the three proteins that constitute LUBAC have separate functions in regulating RIG-I signalling. Both HOIP, the E3 ligase capable of generating M1-ubiquitin chains, and LUBAC accessory protein HOIL-1 are required for viral RNA sensing by RIG-I. The third LUBAC component, SHARPIN, is not required for RIG-I signalling. These data cement the role of LUBAC as a positive regulator of RIG-I signalling and as an important component of antiviral innate immune responses.

immunology↗

bioRxiv2021

Selective modulation of cell surface proteins during vaccinia infection: implications for immune evasion strategies

The interaction between immune cells and virus-infected targets involves multiple plasma membrane (PM) proteins. A systematic study of PM protein modulation by vaccinia virus (VACV), the paradigm of host regulation, has the potential to reveal not only novel viral immune evasion mechanisms, but also novel factors critical in host immunity. Here, >1000 PM proteins were quantified throughout VACV infection, revealing selective downregulation of known T and NK cell ligands including HLA-C, downregulation of cytokine receptors including IFNAR2, IL-6ST and IL-10RB, and rapid inhibition of expression of certain protocadherins and ephrins, candidate activating immune ligands. Downregulation of most PM proteins occurred via a proteasome-independent mechanism. Upregulated proteins included a decoy receptor for TRAIL. Twenty VACV-encoded PM proteins were identified, of which five were not recognised previously as such. Collectively, this dataset constitutes a valuable resource for future studies on antiviral immunity, host-pathogen interaction, poxvirus biology, vector-based vaccine design and oncolytic therapy.

microbiology↗

bioRxiv2021

Smallpox vaccination induces a substantial increase in commensal skin bacteria that promote pathology and enhance immunity

Interactions between pathogens, host microbiota and the immune system influence many physiological and pathological processes. In the 20th century, widespread dermal vaccination with vaccinia virus (VACV) led to the eradication of smallpox but how VACV interacts with the microbiota and whether this influences the efficacy of vaccination are largely unknown. Here we report that intradermal vaccination with VACV induces a large increase in the number of commensal bacteria in infected tissue, which enhance recruitment of inflammatory cells, promote tissue damage and increase immunity. Treatment of vaccinated specific-pathogen-free (SPF) mice with antibiotic, or infection of genetically-matched germ-free (GF) animals caused smaller lesions without alteration in virus titre. Tissue damage correlated with enhanced neutrophil and T cell infiltration and levels of pro-inflammatory tissue cytokines and chemokines. One month after vaccination, GF mice had reduced VACV-neutralising antibodies compared to SPF mice; while numbers of VACV-specific CD8+ T cells were equal in all groups of animals. Thus, skin microbiota may provide an adjuvant-like stimulus during vaccination with VACV. This observation has implications for dermal vaccination with live vaccines. Author SummarySmallpox was caused by variola virus and was eradicated by widespread dermal vaccination with vaccinia virus (VACV), a related orthopoxvirus of unknown origin. Eradication was declared in 1980 without an understanding of the immunological correlates of protection, or knowledge of the effect of smallpox vaccination on the local microbiota. Here we demonstrate that intradermal infection of mice with VACV induces a [~]1000-fold expansion of commensal skin bacteria that influence the recruitment of inflammatory cells into the infected tissue and enhance the size of the vaccination lesion. Antibiotic treatment reduced lesion size without changing virus titres. The bacterial expansion also contributes to the level of neutralizing antibodies at one month post vaccination, because genetically matched germ-free mice developed lower neutralizing antibodies than specific pathogen free controls. Thus, dermal infection by VACV enhanced bacterial growth and these bacteria promote pathology and enhance the antibody response. This finding has implication for dermal vaccination with live vaccines.

microbiology↗

bioRxiv2021

PKR-MEDIATED STRESS RESPONSE ENHANCES DENGUE AND ZIKA VIRUS REPLICATION

The mechanisms by which flaviviruses use non-canonical translation to support their replication in host cells are largely unknown. Here we investigated how the integrated stress response (ISR), which promotes translational arrest by eIF2[a] phosphorylation (p-eIF2[a]), regulates flavivirus replication. During Dengue virus (DENV) and Zika virus (ZIKV) infection, eIF2[a] phosphorylation peaked at 24 hours post infection and was dependent on PKR but not type I interferon. The ISR is activated downstream of p-eIF2 during infection with either virus, but translation arrest only occurred following DENV4 infection. Despite this difference, both DENV4 and ZIKV replication was impaired in cells lacking PKR, independent of IFN-I/NF-kB signalling or cell viability. By using a ZIKV 5' UTR reporter system as a model, we found that this region of the genome is sufficient to promote an enhancement of viral mRNA translation in the presence of an active ISR. Together we provide evidence that flaviviruses escape ISR translational arrest and co-opt this response to increase viral replication.

immunology↗

bioRxiv2020

Chicken cGAS senses fowlpox virus infection and regulates macrophage effector function

The anti-viral immune response is dependent on the ability of infected cells to sense foreign nucleic acids. In multiple species, the pattern recognition receptor (PRR) cyclic GMP-AMP synthase (cGAS) senses viral DNA as an essential component of the innate response. cGAS initiates a range of signalling outputs that are dependent on generation of the second messenger cGAMP that binds to the adaptor protein stimulator of interferon genes (STING). Here we show that in chicken macrophages, the cGAS/STING pathway is essential not only for the production of type-I interferons in response to intracellular DNA stimulation, but also for regulation of macrophage effector functions including the expression of MHC-II and co-stimulatory molecules. In the context of fowlpox, an avian DNA virus infection, the cGAS/STING pathway was found to be responsible for type-I interferon production and MHC-II transcription. The sensing of fowlpox virus DNA is therefore essential for mounting an anti-viral response in chicken cells and for regulation of a specific set of macrophage effector functions.

immunology↗

bioRxiv2020

Shoot-derived miR2111 controls legume root and nodule development

Legumes control their nodule numbers through the Autoregulation Of Nodulation (AON). Rhizobia infection stimulates the production of root-derived CLE peptide hormones that are translocated to the shoot where they regulate a new signal. We used soybean to demonstrate that this shoot-derived signal is miR2111, which is transported via phloem to the root where it targets transcripts of Too Much Love (TML), a negative regulator of nodulation. Shoot perception of rhizobia-induced CLE peptides suppresses miR2111 expression, resulting in TML accumulation in roots and subsequent inhibition of nodule organogenesis. Feeding synthetic mature miR2111 via the petiole increased nodule numbers per plant. Likewise, elevating miR2111 availability by over-expression promoted nodulation, while target mimicry of TML induced the opposite effect on nodule development in wild-type plants and alleviated the supernodulating and stunted root growth phenotypes of AON-defective mutants. Additionally, in non-nodulating wild-type plants, ectopic expression of miR2111 significantly enhanced lateral root emergence with a decrease in lateral root length and average root diameter. In contrast, hairy roots constitutively expressing the target mimic construct exhibited reduced lateral root density. Overall, these findings demonstrate that miR2111 is both the critical shoot-to-root factor that positively regulates root nodule development, and also acts to shape root system architecture via orchestrating the degree of root branching, as well as the length and thickness of lateral roots.

plant biology↗