Endogenous Gene Research Articles

Overexpression of two DELLA subfamily genes MiSLR1 and MiSLR2 from mango promotes early flowering and enhances abiotic stress tolerance in Arabidopsis

Gibberellic acids (GAs) are a group of endogenous phytohormones that play important roles in plant growth and development. SLENDER RICE (SLR) serves as a vital component of the DELLA gene family, which plays an irreplaceable role in regulating plant flowering and height, as well as stress responses. SLR gene has not been reported in mango, and its function is unknown. In present study, two DELLA subfamily genes MiSLR1 and MiSLR2 were identified from mango. MiSLR1 and MiSLR2 were highly expressed in the stems of the juvenile stage, but were expressed at a low level in flower buds and flowers. Gibberellin treatment could up-regulate the expression of MiSLR1 and MiSLR2 genes, but gibberellin biosynthesis inhibitor prohexadione-calcium (Pro-Ca) and paclobutrazol (PAC) treatments significantly down-regulated the expression of MiSLR1, while MiSLR2 was up-regulated. The expression levels of MiSLR1 and MiSLR2 were up-regulated under both salt and drought treatments. Overexpression of MiSLR1 and MiSLR2 genes significantly resulted early flowering in transgenic Arabidopsis and significantly up-regulated the expression levels of endogenous flower-related genes, such as SUPPRESSOR OF CONSTANS1 (SOC1), APETALA1 (AP1), and FRUITFULL (FUL). Interestingly, MiSLR1 significantly reduced the height of transgenic plants, while MiSLR2 gene increased. Overexpression of MiSLR1 and MiSLR2 increased seed germination rate, root length and survival rate of transgenic plants under salt and drought stress. Physiological and biochemical detection showed that the contents of proline (Pro) and superoxide dismutase (SOD) were significantly increased, while the contents of malondialdehyde (MDA) and H2O2 were significantly decreased. Additionally, protein interaction analysis revealed that MiSLR1 and MiSLR2 interacted with several flowering-related and GA-related proteins. The interaction between MiSLR with MiGF14 and MiSOC1 proteins was found for the first time. Taken together, the data showed that MiSLR1 and MiSLR2 in transgenic Arabidopsis both regulated the flowering time and plant height, while also acting as positive regulators of abiotic stress responses.

An efficient inducible model for the control of gene expression in renin cells.

Fate mapping and genetic manipulation of renin cells have relied on either noninducible Cre lines that can introduce the developmental effects of gene deletion or bacterial artificial chromosome transgene-based inducible models that may be prone to spurious and/or ectopic gene expression. To circumvent these problems, we generated an inducible mouse model in which CreERT2 is under the control of the endogenous Akr1b7 gene, an independent marker of renin cells that is expressed in a few extrarenal tissues. We confirmed the proper expression of Cre using Akr1b7CreERT2/+;R26RmTmG/+ mice in which Akr1b7+/renin+ cells become green fluorescent protein (GFP)+ upon tamoxifen administration. In embryos and neonates, GFP was found in juxtaglomerular cells, along the arterioles, and in the mesangium, and in adults, GFP was present mainly in juxtaglomerular cells. In mice treated with captopril and a low-salt diet to induce recruitment of renin cells, GFP extended along the afferent arterioles and in the mesangium. We generated Akr1b7CreERT2/+;Ren1cFl/-;R26RmTmG/+ mice to conditionally delete renin in adult mice and found a marked reduction in kidney renin mRNA and protein and mean arterial pressure in mutant animals. When subjected to a homeostatic threat, mutant mice were unable to recruit renin+ cells. Most importantly, these mice developed concentric vascular hypertrophy ruling out potential developmental effects on the vasculature due to the lack of renin. We conclude that Akr1b7CreERT2 mice constitute an excellent model for the fate mapping of renin cells and for the spatial and temporal control of gene expression in renin cells.NEW & NOTEWORTHY Fate mapping and genetic manipulation are important tools to study the identity of renin cells. Here, we report on a novel Cre mouse model, Akr1b7CreERT2, for the spatial and temporal regulation of gene expression in renin cells. Cre is properly expressed in renin cells during development and in the adult under basal conditions and under physiological stress. Moreover, renin can be efficiently deleted in the adult, leading to the development of concentric vascular hypertrophy.

Abstract P361: Characterization of a Constitutive Adiponectin-Cre Rat Reveals Expression in Adipocyte, Endothelial and Neuronal Lineages

Introduction: The Dahl salt-sensitive (DahlSS) rat is a valuable model for studying hypertension and blood pressure regulation. To create new genetic tools for probing gene function specifically within adipose tissues in this model, we engineered a constitutive Adipoq-Cre rat on a DahlSS genomic background using CRISPR-Cas9 genome editing. Methods: A P2A-Cre cassette was inserted in-frame with the endogenous Adiponectin gene (ENSRNOG00065003537) to enable bicistronic expression from the major transcript (Adipoq-201; ENSRNOT00060022350.1). CRISPR targeting was achieved by microinjecting rat zygotes with a ribonucleoprotein (RNP) complex consisting of Cas9 protein and single guide RNA with a target near the stop codon, and a homology-directed repair plasmid template carrying the Cre recombinase cassette. To evaluate the pattern of Cre expression, Adipoq-Cre DahlSS rats were crossed with a Rosa-CAG-LSL-tdTomato LE reporter line (RRRC#: 009389). The progeny were analyzed for tdTomato reporter expression by cryo-fluorescence tomography (CFT) at postnatal day 10 (P10) and 10 weeks of age, using a Xerra TM EMIT imaging platform (50um sections). A Zeiss LSM 880 system was used to image fresh Vectashield-mounted tissues with a Plan-Apochromat 20x objective and a 561nm laser. Results: Strong CFT signal was detected in all examined adipose depots including subcutaneous, gonadal, and retroperitoneal white adipose tissue, interscapular brown adipose tissue, and perivascular adipose tissue (PVAT). Expression was also detected in the CNS. Confocal imaging of mesenteric PVAT and thoracic aorta PVAT revealed expression in adipocytes, endothelial cells, and peripheral nerves. Conclusion: The newly developed constitutive DahlSS Adipoq-Cre recombinase knockin drives expression in white and brown adipose depots but the presence of expression in non-adipocyte cells suggests either developmental or adult adiponectin expression in endothelial and neuronal lineages, limiting its ability to drive strictly adipose-specific gene expression.

Ca2+-induced CpCBL8-CpCIPK9 module negatively regulates dormancy breaking and cold tolerance in winter-flowering wintersweet

The complex of calcineurin B-like protein (CBL) and CBL-interacting protein kinase (CIPK) serves as key components in calcium-sensing, orchestrating various signals crucial for plant growth, development, and responses to biotic and abiotic stresses. However, the mechanism underlying the response of this module to cold stress and its role in flower development in wintersweet (Chimonanthus praecox) remains unclear. Through expression pattern analysis, calcium ion (Ca2+) concentration assays, correlation analysis, and linear regression analysis, we found that the [Ca2⁺], along with CpCBL8 and CpCIPK9 expression levels in wintersweet flower buds (FBs), significantly decreased during the initial flowering stage when the chilling requirement reached 570 chill units (CU). Notably, there was a significant positive correlation between [Ca2⁺] and CpCBL8 expression. Ca2+ increased the expression of CpCBL8 and CpCIPK9 in FBs, causing a significant delay in the flowering of wintersweet. Furthermore, the function of CpCBL8 was studied using heterologous transformation. Overexpression of CpCBL8 significantly delayed flowering time and significantly reduced cold tolerance and altered the expression pattern of endogenous genes related to low-temperature stress and flower development in transgenic Arabidopsis thaliana. Additionally, transcriptome analysis of chilling-induced dormancy breaking and flower bud enlargement revealed that CpCBL8 and CpCIPK9 were negatively regulated by cold, and the expression pattern of endogenous genes related to flower development and cold stress in wintersweet were similar to that of in A. thaliana. Moreover, protein–protein interaction (PPI) analysis revealed that CpCBL8 and CpCIPK9 interacted in the plasma membrane and nucleus. On the basis of these findings, we speculated that the CpCBL8-CpCIPK9 module plays a crucial role in regulating responses to cold stress and flower development in wintersweet. This study elucidated molecular mechanisms through which the downregulation of the Ca2+-induced CpCBL8-CpCIPK9 module results in dormancy breaking and enhances cold tolerance. This study provides valuable insights for the cultivation of new varieties of wintersweet with increased ornamental value and enhanced cold stress tolerance.

A compact, versatile drug-induced splicing switch system with minimal background expression

Gene-switch techniques hold promising applications in contemporary genetics research, particularly in disease treatment and genetic engineering. Here, we developed a compact drug-induced splicing system that maintains low background using a human ubiquitin C (hUBC) promoter and optimized drug (LMI070) binding sequences based on the Xon switch system. To ensure precise subcellular localization of the protein of interest (POI), we inserted a 2A self-cleaving peptide between the extra N-terminal peptide and POI. This streamlined and optimized switch system, named miniXon2G, effectively regulated POIs in different subcellular localizations both invitro and invivo. Furthermore, miniXon2G could be integrated into endogenous gene loci, resulting in precise, reversible regulation of target genes by both endogenous regulators and drugs. Overall, these findings highlight the performance of miniXon2G in controlling protein expression with great potential for general applicability to diverse biological scenarios requiring precise and delicate regulation.

In silico study of RKD4 gene function in Coffea arabica L. and various cultivated plants related to embryo formation initiation

Arabica coffee supplies 60% of world coffee production because has a unique taste as superior quality beverage. Arabica coffee micropropagation can be conducted by somatic embryogenesis technique which produce clonal, fast dan uniform plant. The somatic embryogenesis (SE) process describes the integration of endogenous signals and gene reprogramming, which releases signals to initiate embryogenic processes. The use of endogenous auxin, either alone or in combination with other PGRs or stress, induces differential gene expression, which modifies the genetic program of somatic cells and regulates the transition to each stage during SE development. The RKD4 gene (RWP-RK DOMAIN-4) is a gene that plays a role in early initiation embryo formation and development. The characterization of RKD4 genes in C. arabica is still limited and under explored. The objective of this research is to explore the characteristics of RKD4 gene by comparing the difference and similarity of RKD4 gene in C. arabica and other cultivated plants. The method was initiate by identifying nucleotide sequences from the National Center for Biotechnology Information (NCBI) database. Furthermore, consists of analysis of nucletide alignment, alignment of amino acid sequences, protein analysis, protein motif functions discovery, analysis of phylogenetic tree, protein 2D and 3D-modelling and physiochemical properties. According to the analysis, there were 100 polymorphism points with a total number of mutations of 211 points. The phylogenetic tree show C. arabica L. has a very close relationship with grapes (Vitis vinivera) based on the RKD4 protein, gene structures and protein motifs. There are nine highly conserved motifs found in the protein alignment. C. arabica L. had more methyl jasmonate element responses than A. thaliana. The findings are useful to understand the intitiation of embryo formation mechanisms of C. arabica L and other cultivate plants during propagation through somatic embryogenesis in the long run.

Involvement of BcNAC083 in 1-MCP-induced delayed yellowing of pak choi (Brassica rapa subsp. Chinensis) through the regulation of reactive oxygen species metabolism and inhibition of major chlorophyll catabolic genes

Leaf yellowing is a typical senescence feature in postharvest pak choi. Plant-specific NAC transcription factors (TFs) are crucial regulators of plant senescence. In this study, a senescence-related NAC TF, BcNAC083, was investigated to identify its transcriptional regulation effects on the yellowing of pak choi by treatment with 1-methylcyclopropene (1-MCP). Applying 5.0 µL L–1 1-MCP alleviated yellowing and maintained a low respiration rate, high chlorophyll content, and relatively complete chloroplast structure in pak choi during storage. However, 10 μL L–1 ethylene accelerated yellowing, as demonstrated by the higher respiration rate, lower chloroplast structural integrity and chlorophyll content. In contrast to ethylene treatment, 1-MCP suppressed the activity of the reactive oxygen species (ROS) metabolism-related enzymes superoxide dismutase (SOD), catalase (CAT), ascorbic peroxidase (APX), and lipoxygenase (LOX), and correspondingly reduced superoxide anion (O2·–), hydrogen peroxide (H2O2), and malondialdehyde (MDA) accumulation. 1-MCP treatment also suppressed the transcript levels of ROS metabolic genes, including BcRBOHC, BcRBOHD, BcSOD, BcCAT, BcAPX, and BcLOX, and inhibited the activity of the chlorophyll catabolic enzymes chlorophyllase (CLH), Mg-de-chelatase, and pheophytin pheophorbide hydrolase (PPH) and transcript levels of associated genes, including BcCLH1/2, BcPPH1/2, BcPAO, BcNYC1, BcSGR1/2, BcHCAR, BcRCCR, and BcCAO. The expression of BcNAC083 was probably induced by ROS and was downregulated by 1-MCP and upregulated by ethylene. Molecular biology experiments determined that BcNAC083 bound directly to and activated the promoters of the chlorophyll metabolism-related genes BcCLH1, BcPPH1, BcNYC1, and BcHCAR. Importantly, transient overexpression of BcNAC083 stimulated the endogenous genes (NbCLH1, NbPPH1, NbNYC1, and NbHCAR) expression in tobacco leaves, resulting in rapid chlorophyll breakdown and leaf degreening. Treatment with 1-MCP may alleviated the yellowing of pak choi by inhibiting ROS accumulation and the transcriptional regulation of BcNAC083, which had positive regulatory effects on major chlorophyll metabolic genes.

Multistep allelic conversion in mouse pre-implantation embryos by AAV vectors

Site-specific recombinases (SSRs) are critical for achieving precise spatiotemporal control of engineered alleles. These enzymes play a key role in facilitating the deletion or inversion of loci flanked by recombination sites, resulting in the activation or repression of endogenous genes, selection markers or reporter elements. However, multiple recombination in complex alleles can be laborious. To address this, a new and efficient method using AAV vectors has been developed to simplify the conversion of systems based on Cre, FLP, Dre and Vika recombinases. In this study, we present an effective method for ex vivo allele conversion using Cre, FLP (flippase), Dre, and Vika recombinases, employing adeno-associated viruses (AAV) as delivery vectors. AAVs enable efficient allele conversion with minimal toxicity in a reporter mouse line. Moreover, AAVs facilitate sequential allele conversion, essential for fully converting alleles with multiple recombination sites, typically found in conditional knockout mouse models. While simple allele conversions show a 100% efficiency rate, complex multiple conversions consistently achieve an 80% conversion rate. Overall, this strategy markedly reduces the need for animals and significantly speeds up the process of allele conversion, representing a significant improvement in genome engineering techniques.

Metabolic engineering of the oleaginous yeast Yarrowia lipolytica for 2-phenylethanol overproduction

The rose fragrance molecule 2-phenylethanol (2-PE) has huge market demand in the cosmetics, food and pharmaceutical industries. However, current 2-PE synthesis methods do not meet the efficiency market requirement. In this study, CRISPR-Cas9-related metabolic engineering strategies were applied to Yarrowia lipolytica for the de novo biosynthesis of 2-PE. Initially, overexpressing exogenous feedback-resistant EcAROGfbr and EcPheAfbr increased 2-PE production to 276.3 mg/L. Subsequently, the ylARO10 and ylPAR4 from endogenous genes were enhanced with the multi-copies to increase the titer to 605 mg/L. Knockout of ylTYR1 and enhancement of shikimate pathway by removing the precursor metabolic bottleneck and overexpressing the genes ylTKT, ylARO1, and ylPHA2 resulted in a significant increase of the 2-PE titer to 2.4 g/L at 84 h, with the yield of 0.06 g/gglu, which is the highest yield for de novo synthesis in yeast. This study provides a valuable precedent for the efficient biosynthesis of shikimate pathway derivatives.

Development of an inducer-free, virulence gene promoter-controlled, and fluorescent reporter-labeled CRISPR interference system in Staphylococcus aureus.

The dCas9-based Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) interference (CRISPRi) gene regulation technique requires two components: a catalytically inactive Cas9 protein (dCas9) and a single-guide RNA that targets the gene of interest. This system is commonly activated by expressing dCas9 through an inducible gene promoter, but these inducers may affect cellular physiology, and accessibility and permeability of the inducer are limited in relevant model systems. Here, we have developed an alternative approach for CRISPRi activation in the clinical isolate Staphylococcus aureus USA300 LAC, where dCas9 was expressed through endogenous virulence gene promoters (vgp); coagulase, autolysin, or fibronectin-binding protein A. Additionally, we integrated a fluorescent reporter gene into the vgp-CRISPRi system to monitor the activity of the dcas9-controlling promoter. Testing the efficacy of vgp-CRISPRi by inducing growth arrest (when targeting penicillin-binding protein 1), downregulating target gene expression, or blocking coagulase-dependent coagulation of blood plasma, we provide a proof-of-concept demonstration that the virulence gene promoter-driven CRISPRi system is functional in S. aureus.IMPORTANCEThe presented inducer-free, endogenous virulence gene promoter-induced, dCas9-based Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) interference (CRISPRi system addresses several shortcomings related to the use of inducer-dependent systems such as effects on cell physiology or limitations in permeability, and it avoids the high, putatively toxic levels of dCas9 in CRISPRi systems controlled by strong, constitutive promoters.

Optimizing ABA-based chemically induced proximity for enhanced intracellular transcriptional activation and modification response to ABA.

Abscisic acid (ABA)-based chemically induced proximity (CIP) is primarily mediated by the interaction of the ABA receptor pyrabactin resistance 1-like 1 (PYL1) and the 2C-type protein phosphatase ABI1, which confers ABA-induced proximity to their fusion proteins, and offers precise temporal control of a wide array of biological processes. However, broad application of ABA-based CIP has been limited by ABA response intensity. In this study, we demonstrated that ABA-induced interaction between another ABA receptor pyrabactin resistance 1 (PYR1) and ABI1 exhibited higher ABA response intensity than that between PYL1 and ABI1 in HEK293T cells. We engineered PYR1-ABI1 and PYL1-ABI1 into ABA-induced transcriptional activation tools in mammalian cells by integration with CRISPR/dCas9 and found that the tool based on PYR1-ABI1 demonstrated better ABA response intensity than that based on PYL1-ABI1 for both exogenous and endogenous genes in mammalian cells. We further achieved ABA-induced RNA m6A modification installation and erasure by combining ABA-induced PYR1-ABI1 interaction with CRISPR/dCas13, successfully inhibiting tumor cell proliferation. We subsequently improved the interaction of PYR1-ABI1 through phage-assisted continuous evolution (PACE), successfully generating a PYR1 mutant (PYR1m) whose interaction with ABI1 exhibited a higher ABA response intensity than that of the wild-type. In addition, we tested the transcriptional activation tool based on PYRm-ABI1 and found that it also showed a higher ABA response intensity than that of the wild type. These results demonstrate that we have developed a novel ABA-based CIP and further improved upon it using PACE, providing a new approach for the modification of other CIP systems.

Microbial assimilatory sulfate reduction-mediated H2S: an overlooked role in Crohn’s disease development

BackgroundH2S imbalances in the intestinal tract trigger Crohn's disease (CD), a chronic inflammatory gastrointestinal disorder characterized by microbiota dysbiosis and barrier dysfunction. However, a comprehensive understanding of H2S generation in the gut, and the contributions of both microbiota and host to systemic H2S levels in CD, remain to be elucidated. This investigation aimed to enhance comprehension regarding the sulfidogenic potential of both the human host and the gut microbiota.ResultsOur analysis of a treatment-naive CD cohorts' fecal metagenomic and biopsy metatranscriptomic data revealed reduced expression of host endogenous H2S generation genes alongside increased abundance of microbial exogenous H2S production genes in correlation with CD. While prior studies focused on microbial H2S production via dissimilatory sulfite reductases, our metagenomic analysis suggests the assimilatory sulfate reduction (ASR) pathway is a more significant contributor in the human gut, given its high prevalence and abundance. Subsequently, we validated our hypothesis experimentally by generating ASR-deficient E. coli mutants ∆cysJ and ∆cysM through the deletion of sulfite reductase and L-cysteine synthase genes. This alteration significantly affected bacterial sulfidogenic capacity, colon epithelial cell viability, and colonic mucin sulfation, ultimately leading to colitis in murine model. Further study revealed that gut microbiota degrade sulfopolysaccharides and assimilate sulfate to produce H2S via the ASR pathway, highlighting the role of sulfopolysaccharides in colitis and cautioning against their use as food additives.ConclusionsOur study significantly advances understanding of microbial sulfur metabolism in the human gut, elucidating the complex interplay between diet, gut microbiota, and host sulfur metabolism. We highlight the microbial ASR pathway as an overlooked endogenous H2S producer and a potential therapeutic target for managing CD.Dka3P5uGJeBhH66pkNJcogVideo

A portable multifunctional biosensor based on a newly screened endogenous reference gene for pork adulteration detection

The adulteration of animal-derived food is a widespread problem with meat adulteration emerging as a global concern. To address the need for on-site rapid detection and visual analysis, a portable multifunction biosensor (PMB) was developed. This device integrates Recombinase Polymerase Amplification (RPA), CRISPR/Cas12a assay, and a custom-designed 3D-printed multifunction device, specifically for the visual and rapid detection of pork in food. Initially, a screening model was constructed using Perl bioinformatics based on chromosomal gene information, and the LOC110262058 gene was selected as a reliable endogenous reference gene for pigs. Subsequently, a one-tube RPA-CRISPR/Cas12a system was established to simplify the procedures, converting pork-specific signals into fluorescence while preventing cross-contamination. In addition, an independently designed 3D-printed multifunction device was developed to support the RPA-CRISPR/Cas12a system for one-tube detection, incorporating functions such as heating, centrifugation, and imaging. The reaction conditions of the PMB were optimized to reduce the reaction time to 20–30 min with a sensitivity of 0.01 g/100 g. The analysis of actual samples indicated that the PMB has high selectivity and practical effectiveness for pork detection. The proposed biosensor offers several detection advantages, including output, ease of use, stability, and independence from complex equipment, making it a powerful method for rapid pork detection in food.

FaNPR3 Members of the NPR1-like Gene Family Negatively Modulate Strawberry Fruit Resistance against Colletotrichum acutatum.

Strawberry fruit is highly appreciated worldwide for its organoleptic and healthy properties. However, this plant is attacked by many pathogenic fungi, which significantly affect fruit production and quality at pre- and post-harvest stages, making chemical applications the most effective but undesirable strategy to control diseases that has been found so far. Alternatively, genetic manipulation, employing plant key genes involved in defense, such as members of the NPR-like gene family, has been successful in many crops to improve resistance. The identification and use of the endogenous counterpart genes in the plant of interest (as it is the case of strawberry) is desirable as it would increase the favorable outcome and requires prior knowledge of their defense-related function. Using RNAi technology in strawberry, transient silencing of Fragaria ananassa NPR3 members in fruit significantly reduced tissue damage after Colletotrichum acutatum infection, whereas the ectopic expression of either FaNPR3.1 or FaNPR3.2 did not have an apparent effect. Furthermore, the ectopic expression of FaNPR3.2 in Arabidopsis thaliana double-mutant npr3npr4 reverted the disease resistance phenotype to Pseudomonas syringe to wild-type levels. Therefore, the results revealed that members of the strawberry FaNPR3 clade negatively regulate the defense response to pathogens, as do their Arabidopsis AtNPR3/AtNPR4 orthologs. Also, evidence was found showing that FaNPR3 members act in strawberry (F. ananassa) as positive regulators of WRKY genes, FaWRKY19 and FaWRKY24; additionally, in Arabidopsis, FaNPR3.2 negatively regulates its orthologous genes AtNPR3/AtNPR4. We report for the first time the functional characterization of FaNPR3 members in F. ananassa, which provides a relevant molecular basis for the improvement of resistance in this species through new breeding technologies.

Transcription of HIV-1 at sites of intact latent provirus integration.

HIV-1 antiretroviral therapy is highly effective but fails to eliminate a reservoir of latent proviruses, leading to a requirement for life-long treatment. How the site of integration of authentic intact latent proviruses might impact their own or neighboring gene expression or reservoir dynamics is poorly understood. Here, we report on proviral and neighboring gene transcription at sites of intact latent HIV-1 integration in cultured T cells obtained directly from people living with HIV, as well as engineered primary T cells and cell lines. Proviral gene expression was correlated to the level of endogenous gene expression under resting but not activated conditions. Notably, latent proviral promoters were 100-10,000× less active than in productively infected cells and had little or no measurable impact on neighboring gene expression under resting or activated conditions. Thus, the site of integration has a dominant effect on the transcriptional activity of intact HIV-1 proviruses in the latent reservoir, thereby influencing cytopathic effects and proviral immune evasion.

Rice A20/AN1 protein, OsSAP10, confers water-deficit stress tolerance via proteasome pathway and positive regulation of ABA signaling in Arabidopsis.

Overexpression of rice A20/AN1 zinc-finger protein, OsSAP10, improves water-deficit stress tolerance in Arabidopsis via interactionwith multiple proteins. Stress-associated proteins (SAPs) constitute a class of A20/AN1 zinc-finger domain containing proteins and their genes are induced in response to multiple abiotic stresses. The role of certain SAP genes in conferring abiotic stress tolerance is well established, but their mechanism of action is poorly understood. To improve our understanding of SAP gene functions, OsSAP10, a stress-inducible rice gene, was chosen for the functional and molecular characterization. To elucidate its role in water-deficit stress (WDS) response, we aimed to functionally characterize its roles in transgenic Arabidopsis, overexpressing OsSAP10. OsSAP10 transgenics showed improved tolerance to water-deficit stress at seed germination, seedling and mature plant stages. At physiological and biochemical levels, OsSAP10 transgenics exhibited a higher survival rate, increased relative water content, high osmolyte accumulation (proline and soluble sugar), reduced water loss, low ROS production, low MDA content and protected yield loss under WDS relative to wild type (WT). Moreover, transgenics were hypersensitive to ABA treatment with enhanced ABA signaling and stress-responsive genes expression. The protein-protein interaction studies revealed that OsSAP10 interacts with proteins involved in proteasomal pathway, such as OsRAD23, polyubiquitin and with negative and positive regulators of stress signaling, i.e., OsMBP1.2, OsDRIP2, OsSCP and OsAMTR1. The A20 domain was found to be crucial for most interactions but insufficient for all interactions tested. Overall, our investigations suggest that OsSAP10 is an important candidate for improving water-deficit stress tolerance in plants, and positively regulates ABA and WDS signaling via protein-protein interactions and modulation of endogenous genes expression in ABA-dependent manner.

Conditional RNA interference in mammalian cells via RNA transactivation

RNA interference (RNAi) is a powerful tool for sequence-specific gene knockdown in therapeutic and research applications. However, spatiotemporal control of RNAi is required to decrease nonspecific targeting, potential toxicity, and allow targeting of essential genes. Herein we describe a class of de-novo-designed RNA switches that enable sequence-specific regulation of RNAi in mammalian cells. Using cis-repressing RNA elements, we engineer RNA devices that only initiate microRNA biogenesis when binding with cognate trigger RNAs. We demonstrate that this conditional RNAi system, termed Orthogonal RNA Interference induced by Trigger RNA (ORIENTR), provides up to 14-fold increases in artificial miRNA biogenesis upon activation in orthogonal libraries. We show that integration of ORIENTR triggers with dCas13d enhances dynamic range to up to 31-fold. We further demonstrate that ORIENTR can be applied to detect endogenous RNA signals and to conditionally knockdown endogenous genes, thus enabling regulatory possibilities including cell-type-specific RNAi and rewiring of transcriptional networks via RNA profile.

Functional plasticity of HCO3– uptake and CO2 fixation in Cupriavidus necator H16

Despite its prominence, the ability to engineer Cupriavidus necator H16 for inorganic carbon uptake and fixation is underexplored. We tested the roles of endogenous and heterologous genes on C. necator inorganic carbon metabolism. Deletion of β-carbonic anhydrase can had the most deleterious effect on C. necator autotrophic growth. Replacement of this native uptake system with several classes of dissolved inorganic carbon (DIC) transporters from Cyanobacteria and chemolithoautotrophic bacteria recovered autotrophic growth and supported higher cell densities compared to wild-type (WT) C. necator in batch culture. Strains expressing Halothiobacillus neopolitanus DAB2 (hnDAB2) and diverse rubisco homologs grew in CO2 similarly to the wild-type strain. Our experiments suggest that the primary role of carbonic anhydrase during autotrophic growth is to support anaplerotic metabolism, and an array of DIC transporters can complement this function. This work demonstrates flexibility in HCO3– uptake and CO2 fixation in C. necator, providing new pathways for CO2-based biomanufacturing.

An engineered citrus tristeza virus (T36CA)-based vector induces gene-specific RNA silencing and is graft transmissible to commercial citrus varieties.

A protein-expressing citrus tristeza virus (CTV)-based vector construct, pT36CA-V1.3, obtained from a California isolate of the T36 strain (T36CA), was retooled into a virus induced gene silencing (VIGS) system intended for use with studies of California citrus. VIGS constructs engineered with a truncated Citrus macrophylla (Cm) PHYTOENE DESATURASE (PDS) gene sequence in the sense or anti-sense orientation worked equally well to silence the endogenous CmPDS gene. In a parallel effort to optimize vector performance, two non-synonymous nucleotides in open reading frame 1a of pT36CA-V1.3 were replaced with those conserved in the reference sequences from the T36CA cDNA library. The resulting viruses, T36CA-V1.4 (with one amino acid modification: D760N) and T36CA-V1.5 (with two amino acid modifications: D760N and P1174L), along with T36CA-V1.3 were individually propagated in Nicotiana benthamiana and C. macrophylla plants. Enzyme-linked immunosorbent assay (ELISA) measurements of extracts of the newly emerged leaves suggested that all three viruses accumulated to similar levels in N. benthamiana plants at 5 week-post-inoculation. ELISA values of T36CA-V1.4- and -V1.5-infected C. macrophylla samples were significantly higher than that of T36CA-V1.3-infected samples within an 8 to 12 month-post-inoculation (mpi) window, suggesting a higher accumulation of T36CA-V1.4 and -V1.5 than T36CA-V1.3. However, at 36 mpi, the ELISA values suggested that all three viruses accumulated to similar levels. When C. macrophylla plants infected with each of the three viruses were grafted to commercial citrus varieties, a limited number of receptor plants became infected, demonstrating a weak but nonetheless (the first) successful delivery of T36CA to California-grown commercial citrus.

Human induced pluripotent stem cells for live cell cycle monitoring and endogenous gene activation

The fluorescence ubiquitination cell cycle inhibitor (FUCCI) has been introduced to monitor cell cycle activity in living cells, including human induced pluripotent stem cells (hiPSC) and derived cell types. We have recently developed hiPSC with stable expression of dCas9VPR for endogenous gene activation and a Citrine-tagged ACTN2 cell line to monitor sarcomere development and function in muscle cells. Here, we present dual and triple transgenic hiPSC lines developed by genomic integration of FUCCI with and without dCas9VPR into the ROSA26 and AAVS1 loci, respectively, in the previously introduced ACTN2-Citrine line. Functionality of the transgenes was demonstrated in the novel hiPSC line, which we introduce as Myo-CCER and CraCCER.