Biology subjects

Sederoff, H.

Publications and source records attributed to Sederoff, H..

7 recordsLinked to original sources

bioRxiv2026

Identification of Potential Regulatory Non-Coding RNAs in Lotus Japonicus Symbiosis

O_LISymbiosis between legumes and rhizobia is beneficial on nutrient-poor soils, as it enables the fixation of atmospheric N2. To establish this symbiosis, gene expression in both the host plant and the symbiont has to be regulated. To understand the underlying RNA-mediated regulation of host gene expression, we designed experiments to identify competing endogenous networks involving circular RNA, microRNA, and linear transcripts during symbiosis, using wt and symbiosis-deficient Lotus japonicus mutants with the rhizobium Mesorhizobium loti (M. loti). C_LIO_LICircRNA, miRNA, and linear transcripts were identified from Lotus japonicus wildtype and CCamK mutant (ccamk-13; snf-1) seedlings without inoculation or with M. loti inoculation using deep short-read sequencing with rRNA-depletion and random primers. C_LIO_LIDifferentially expressed miRNAs showed negative correlations to predicted target genes and may regulate symbiotic processes. The symbiosis essential iron-sensor LjnsRING/BRUTUS expresses a circRNA which was upregulated in symbiotic treatments. This circRNA may act as a target mimic and contribute to nodule longevity. CircRNAs are predicted to act predominantly as trans-regulatory molecules with similar frequencies in Arabidopsis thaliania, Oryza sativa, and Lotus japonicus. C_LIO_LIWe identified novel miRNAs, long noncoding RNAs, and circRNAs, and nominated several as potential new regulatory non-coding RNAs that may act as target mimics to stabilize genes and support symbiosis. C_LI SummarySymbiosis between Lotus japonicus and Mesorhizobium loti involves treatment-specific regulation of competing endogenous RNA networks involving circular RNA, miRNA, and linear transcripts.

plant biology↗

bioRxiv2025

Circular RNAs in Lotus japonicus Responses to Nutrient Supply and Symbiotic Interactions

Symbiotic relationships, such as those formed between legumes and rhizobia or arbuscular mycorrhizal (AM) fungi, function by enhancing the nutrient uptake into the plant. The establishment and coordination of the symbiotic interactions requires changes in gene expression in the host and microbe. Circular RNAs (circRNAs) can function through sponging of microRNAs (miRNAs), resulting in changes in transcript abundances. We identified 15,252 unique nuclear circRNAs in Lotus japonicus under different nutrient conditions and symbiotic interactions with rhizobia or AMF. Our results revealed treatment-specific circRNAs and circRNAs originating from key genes in the Common Symbiosis Pathway, suggesting their potential role in the establishment of these symbioses. We validated select circRNAs potentially involved in the regulation of symbiosis and predicted miRNA recognition elements (MREs) that were only created by the backsplice junction of circRNAs. Backsplice-generated MREs represent an additional mechanism through which circRNAs may modulate abundances and translation of mRNAs. Our sequencing approach using random hexamer primers also enabled us to simultaneously characterize the transcriptome of the symbionts and host.

plant biology↗

bioRxiv2024

Camelina CircRNA Landscape: Implications for Gene Regulation and Fatty Acid Metabolism

Circular RNAs (circRNAs) are closed-loop RNAs forming a covalent bond between their 3 and 5 ends, the backsplice junction (BSJ), rendering them resistant to exonucleases and thus more stable compared to linear RNAs. Identification of circRNAs and distinction from its cognate linear RNA is only possible by sequencing the BSJ that is unique to the circRNA. CircRNAs are involved in regulation of their cognate RNAs by increasing transcription rates, RNA stability and alternative splicing. We have identified circRNAs from Camelina sativa that are associated with the regulation of germination, light response, and lipid metabolism. We sequenced light-grown and etiolated seedlings after 5 or 7 days post-germination and identified a total of 3,447 circRNAs from 2,763 genes. Most circRNAs originate from a single homeolog of the three subgenomes from allohexaploid camelina and correlates with higher ratios of alternative splicing of their cognate genes. A network analysis shows the interactions of select miRNA:circRNA:mRNAs for regulation of transcript stabilities where circRNA can act as a competing endogenous RNA. Several key lipid metabolism genes can generate circRNA and we confirmed the presence of KASII circRNA as a true circRNA. CircRNA in camelina can be a novel target for breeding and engineering efforts. Core ideasO_LIFirst discovery of 3,447 genic and 307 intergenic unique putative circRNAs from Camelina sativa. C_LIO_LIWe identified circRNAs that were regulated in response to seedling de-etiolation. C_LIO_LIMost circRNAs originate from only one homeolog of the three subgenomes in this allohexaploid Camelina. C_LIO_LIAlternative splicing of exon skipping and intron retention positively correlate with circRNA occurrence. C_LIO_LIValidation of KASII circRNAs as an example of lipid metabolism pathways potentially regulated by circRNA. C_LI

plant biology↗

bioRxiv2023

Re-engineering a lost trait: IPD3, a master regulator of arbuscular mycorrhizal symbiosis, affects genes for immunity and metabolism of non-host Arabidopsis when restored long after its evolutionary loss

Arbuscular mycorrhizal symbiosis (AM) is a beneficial trait originating with the first land plants, which has subsequently been lost by species scattered throughout the radiation of plant diversity to the present day, including the model Arabidopsis thaliana. To explore why an apparently beneficial trait would be repeatedly lost, we generated Arabidopsis plants expressing a constitutively active form of Interacting Protein of DMI3, a key transcription factor that enables AM within the Common Symbiosis Pathway, which was lost from Arabidopsis along with the AM host trait. We characterize the transcriptomic effect of expressing IPD3 in Arabidopsis with and without exposure to the AM fungus (AMF) Rhizophagus irregularis, and compare these results to the AM model Lotus japonicus and its ipd3 knockout mutant cyclops-4. Despite its long history as a non-AM species, restoring IPD3 in the form of its constitutively active DNA-binding domain to Arabidopsis altered expression of specific gene networks. Surprisingly, the effect of expressing IPD3 in Arabidopsis and knocking it out in Lotus was strongest in plants not exposed to AMF, which is revealed to be due to changes in IPD3 genotype causing a transcriptional state which partially mimics AMF exposure in non-inoculated plants. Our results indicate that despite the long interval since loss of AM and IPD3 in Arabidopsis, molecular connections to symbiosis machinery remain in place in this nonAM species, with implications for both basic science and the prospect of engineering this trait for agriculture.

plant biology↗

bioRxiv2022

Diversity, Phylogenetic Relationships, And Expression Profiles Of Invertase Inhibitor Genes In Sweetpotato

Invertases and their inhibitor proteins are key regulators of carbon allocation in plants. Manipulation of invertase inhibitor (ITI) activity can potentially increase crop yield. The aim of this study was to determine the sequence diversity, phylogenetic relationships, and expression profiles of ITI genes in sweetpotato(Ipomoea batatas).. The coding sequences of two ITI paralogs (SPITI1 and SPITI2) were cloned from two sweetpotato varieties (Beauregard and Jewel) and sequenced. The DNA sequences were used to deduce amino acids sequences and predicted protein properties. Quantitative PCR (qPCR) was carried out to study the expression profiles of the genes at different developmental stages. The results show that introns are absent in both SPITI paralogs. SNPs, Indels, and variable simple sequence repeats (SSR) were present in the SPITI1 paralog, however, only SNPs were identified in the SPITI2 paralog. The predicted SPITI1 protein had 168, 172, or 174 amino acid residues, and molecular weights ranging from 17.88 to 18.38 kDa. In contrast, SPITI2 coded for a protein with 192 amino acid residues, with molecular weight ranging from 20.59 to 20.65 kDa. All conserved domains of ITI proteins were present in both protein isoforms. Phylogenetic analysis indicated that SPITI genes were more closely related to I.trifida and I.triloba than I.nil, thus, suggesting their evolutionary relationship and conservation. A qPCR study indicated that both SPITI genes were expressed in all the sample tissues, though relative expression values differed across tissues at different developmental stages. This is the first study reporting diversity of SPITI genes and of an ~18 kDA isoform in sweetpotato. The findings may enable design of genetic engineering strategies for SPITI genes, including CRISPR/Cas gene editing in sweetpotato.

molecular biology↗

bioRxiv2022

Beyond energy balance in agrivoltaic food production: Emergent crop traits from color selective solar cells

The integration of semi-transparent organic solar cells (ST-OSCs) in greenhouses offers new agrivoltaic opportunities to meet the growing demands for sustainable food production. The tailored absorption/transmission spectra of ST-OSCs impacts the power generated as well as crop growth, development and responses to the biotic and abiotic environments. We grew lettuce and tomato, traditional greenhouse crops, under three ST-OSC filters that create different light spectra. Lettuce yield and early tomato development are not negatively affected by the modified light environment. Our genomic analysis reveals that lettuce production exhibits beneficial traits involving nutrient content and nitrogen utilization while select ST-OSCs impact regulation of flowering initiation in tomato. ST-OSCs integrated into greenhouses are not only a promising technology for energy-neutral, sustainable and climate-change protected crop production, but can deliver benefits beyond energy considerations.

plant biology↗

bioRxiv2022

Introduction of a condensed, reverse tricarboxylic acid cycle for additional CO2 fixation in plants

Plants employ the Calvin-Benson cycle (CBC) to fix atmospheric CO2 for the production of biomass. The flux of carbon through the CBC is limited by the activity and selectivity of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Alternative pathways that do not use RuBisCO to fix CO2 exist but occur only in anaerobic microorganisms. Rather than modifying existing routes of carbon metabolism in plants, we have developed a synthetic carbon fixation cycle that does not exist in nature, but is inspired by metabolisms of bacterial autotrophs. This synthetic cycle uses endogenous plant metabolites to fix CO2 and yield glyoxylate as a product. In this work, we build and characterize a condensed, reverse tricarboxylic acid (crTCA) cycle in vitro and in planta. We demonstrate that a simple, synthetic cycle can be used to fix carbon in vitro under aerobic and mesophilic conditions and that these enzymes retain activity when expressed transiently in planta. We then evaluate stable transgenic lines of Camelina sativa that have both phenotypic and physiologic changes. Transgenic C. sativa are shorter than controls with increased rates of photosynthetic CO2 assimilation and changes in photorespiratory metabolism. This first iteration of a build-test-learn phase of the crTCA cycle provides promising evidence that this pathway can be used to increase photosynthetic capacity in plants.

plant biology↗