Inter-species functional compatibility of the Theobroma cacao and Arabidopsis FT orthologs: 90 million years of functional conservation of meristem identity genes

Abstract Background In angiosperms the transition to flowering is controlled by a complex set of interacting networks integrating a range of developmental, physiological, and environmental factors optimizing transition time for maximal reproductive efficiency. The molecular mechanisms comprising these networks have been partially characterized and include both transcriptional and post-transcriptional regulatory pathways. Florigen, encoded by FLOWERING LOCUS T (FT) orthologs, is a conserved central integrator of several flowering time regulatory pathways. To characterize the molecular mechanisms involved in controlling cacao flowering time, we have characterized a cacao candidate florigen gene, TcFLOWERING LOCUS T (TcFT). Understanding how this conserved flowering time regulator affects cacao plant’s transition to flowering could lead to strategies to accelerate cacao breeding. Results BLAST searches of cacao genome reference assemblies identified seven candidate members of the CENTRORADIALIS/TERMINAL FLOWER1/SELF PRUNING gene family including a single florigen candidate. cDNA encoding the predicted cacao florigen was cloned and functionally tested by transgenic genetic complementation in the Arabidopsis ft-10 mutant. Transgenic expression of the candidate TcFT cDNA in late flowering Arabidopsis ft-10 partially rescues the mutant to wild-type flowering time. Gene expression studies reveal that TcFT is spatially and temporally expressed in a manner similar to that found in Arabidopsis, specifically, TcFT mRNA is shown to be both developmentally and diurnally regulated in leaves and is most abundant in floral tissues. Finally, to test interspecies compatibility of florigens, we transformed cacao tissues with AtFT resulting in the remarkable formation of flowers in tissue culture. The morphology of these in vitro flowers is normal, and they produce pollen that germinates in vitro with high rates. Conclusion We have identified the cacao CETS gene family, central to developmental regulation in angiosperms. The role of the cacao’s single FT-like gene (TcFT) as a general regulator of determinate growth in cacao was demonstrated by functional complementation of Arabidopsis ft-10 late-flowering mutant and through gene expression analysis. In addition, overexpression of AtFT in cacao resulted in precocious flowering in cacao tissue culture demonstrating the highly conserved function of FT and the mechanisms controlling flowering in cacao.

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Cell–cell coupling and DNA methylation abnormal phenotypes in the after-hours mice

Epigenetics & Chromatin ◽

10.1186/s13072-020-00373-5 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Federico Tinarelli ◽

Elena Ivanova ◽

Ilaria Colombi ◽

Erica Barini ◽

Edoardo Balzani ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Neuronal Networks ◽

Molecular Mechanisms ◽

Ex Vivo ◽

Neuronal Cultures ◽

Functional Impairments ◽

After Hours ◽

The Impact

Abstract Background DNA methylation has emerged as an important epigenetic regulator of brain processes, including circadian rhythms. However, how DNA methylation intervenes between environmental signals, such as light entrainment, and the transcriptional and translational molecular mechanisms of the cellular clock is currently unknown. Here, we studied the after-hours mice, which have a point mutation in the Fbxl3 gene and a lengthened circadian period. Methods In this study, we used a combination of in vivo, ex vivo and in vitro approaches. We measured retinal responses in Afh animals and we have run reduced representation bisulphite sequencing (RRBS), pyrosequencing and gene expression analysis in a variety of brain tissues ex vivo. In vitro, we used primary neuronal cultures combined to micro electrode array (MEA) technology and gene expression. Results We observed functional impairments in mutant neuronal networks, and a reduction in the retinal responses to light-dependent stimuli. We detected abnormalities in the expression of photoreceptive melanopsin (OPN4). Furthermore, we identified alterations in the DNA methylation pathways throughout the retinohypothalamic tract terminals and links between the transcription factor Rev-Erbα and Fbxl3. Conclusions The results of this study, primarily represent a contribution towards an understanding of electrophysiological and molecular phenotypic responses to external stimuli in the Afh model. Moreover, as DNA methylation has recently emerged as a new regulator of neuronal networks with important consequences for circadian behaviour, we discuss the impact of the Afh mutation on the epigenetic landscape of circadian biology.

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Serial analysis of gene expression (SAGE) during porcine embryo development

Reproduction Fertility and Development ◽

10.1071/rd03081 ◽

2004 ◽

Vol 16 (2) ◽

pp. 87 ◽

Cited By ~ 12

Author(s):

Le Ann Blomberg ◽

Kurt A. Zuelke

Keyword(s):

Gene Expression ◽

Functional Genomics ◽

Embryo Development ◽

Molecular Mechanisms ◽

Physiological Role ◽

Transgenic Animals ◽

Specific Gene ◽

Research Strategies

Functional genomics provides a powerful means for delving into the molecular mechanisms involved in pre-implantation development of porcine embryos. High rates of embryonic mortality (30%), following either natural mating or artificial insemination, emphasise the need to improve the efficiency of reproduction in the pig. The poor success rate of live offspring from in vitro-manipulated pig embryos also hampers efforts to generate transgenic animals for biotechnology applications. Previous analysis of differential gene expression has demonstrated stage-specific gene expression for in vivo-derived embryos and altered gene expression for in vitro-derived embryos. However, the methods used to date examine relatively few genes simultaneously and, thus, provide an incomplete glimpse of the physiological role of these genes during embryogenesis. The present review will focus on two aspects of applying functional genomics research strategies for analysing the expression of genes during elongation of pig embryos between gestational day (D) 11 and D12. First, we compare and contrast current methodologies that are being used for gene discovery and expression analysis during pig embryo development. Second, we establish a paradigm for applying serial analysis of gene expression as a functional genomics tool to obtain preliminary information essential for discovering the physiological mechanisms by which distinct embryonic phenotypes are derived.

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GENE EXPRESSION DURING INDIRECT SOMATIC EMBRYOGENESIS OF PLANTS

Proceedings of the Nova Scotian Institute of Science (NSIS) ◽

10.15273/pnsis.v42i2.3614 ◽

2004 ◽

Vol 42 (2) ◽

Author(s):

Tammy Estabrooks ◽

Zhongmin Dong

Keyword(s):

Gene Expression ◽

Somatic Embryogenesis ◽

Embryo Development ◽

Current Literature ◽

Molecular Mechanisms ◽

Indirect Somatic Embryogenesis ◽

Experimental Tool ◽

Plant Embryo ◽

Plant Embryo Development

Somatic embryogenesis is the process by which somatic cells are induced into an embryogenic state, followed by differentiation into embryos. Somatic embryogenesis, in addition to being a method of propagation, can serve as an experimental tool for research into plant embryo development. This is a review of the current literature on in vitro plant somatic embryogenesis and the molecular advances made to identify genes expressed during the various stages of this process. Some factors hindering the elucidation of the molecular mechanisms underlying somatic embryogenesis are discussed.L’embryogenèse somatique est le processus par lequel les cellules somatiques passent à l’état embryogène et se différencient en embryons. En plus de constituer une méthode de propagation, elle peut servir d’outil expérimental de recherche pour développer des embryons de plantes. Le présent document est une revue de la documentation sur l’embryogenèse somatique végétale in vitro et sur les progrès réalisés à l’échelle moléculaire pour identifier les gènes exprimés au cours des divers stades du processus. On examine aussi certains facteurs qui rendent difficile l’élucidation des mécanismes moléculaires de l’embryogenèse somatique.

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Methylation pattern polymorphism of cyp19a in Nile tilapia and hybrids

Open Life Sciences ◽

10.1515/biol-2018-0040 ◽

2018 ◽

Vol 13 (1) ◽

pp. 327-334 ◽

Cited By ~ 1

Author(s):

Xiaowu Chen ◽

Yonghua Zhao ◽

Yudong He ◽

Jinliang Zhao

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Methylation Level ◽

Molecular Mechanisms ◽

Methylation Pattern ◽

Male Ratio ◽

Sex Development ◽

Pattern Polymorphism ◽

Fish Hybrids

AbstractSkewed sex development is prevalent in fish hybrids. However, the histological observation and molecular mechanisms remain elusive. In this study, we showed that the interspecific hybrids of the two fish species, Oreochromis niloticus and Oreochromis aureus, had a male ratio of 98.02%. Microscopic examination revealed that the gonads of both male and female hybrids were developmentally retarded. Compared with the ovaries, the testes of both O. niloticus and hybrids showed higher DNA methylation level in two selected regions in the promoter of cyp19a, the gonadal aromatase gene that converts androgens into estrogens, cyp19a showed higher level gene expression in the ovary than in the testis in both O. niloticus and hybrid tilapia. Methylation and gene expression level of cyp19a were negative correlation between the testis and ovary. Gene transcription was suppressed by the methylation of the cyp19a promoter in vitro. While there is no obvious difference of the methylation level in testis or ovary between O. niloticus and hybrids. Thus, the DNA methylation of the promoter of cyp19a may be an essential component of the sex maintenance, but not a determinant of high male ratio and developmental retardation of gonads in tilapia hybrids.

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Human urine alters methicillin-resistant Staphylococcus aureus virulence and transcriptome

Applied and Environmental Microbiology ◽

10.1128/aem.00744-21 ◽

2021 ◽

Author(s):

Santosh Paudel ◽

Kamal Bagale ◽

Swapnil Patel ◽

Nicholas J. Kooyers ◽

Ritwij Kulkarni

Keyword(s):

Gene Expression ◽

Staphylococcus Aureus ◽

Urinary Tract ◽

Urinary Tract Infections ◽

Human Urine ◽

Molecular Mechanisms ◽

Methicillin Resistant ◽

Life Threatening ◽

Tract Infections

Gram-positive methicillin-resistant Staphylococcus aureus (MRSA) is an emerging cause of hospital-associated urinary tract infections (UTI), especially in catheterized individuals. Despite being rare, MRSA UTI are prone to potentially life-threatening exacerbations such as bacteremia that can be refractory to routine antibiotic therapy. To delineate the molecular mechanisms governing MRSA urinary pathogenesis, we exposed three S. aureus clinical isolates, including two MRSA strains to human urine for 2h and analyzed virulence characteristics and changes in gene expression. The in vitro virulence assays showed that human urine rapidly alters adherence to human bladder epithelial cells and fibronectin, hemolysis of sheep RBCs, and surface hydrophobicity in a staphylococcal strain-specific manner. In addition, RNA-Seq analysis of uropathogenic strain MRSA-1369 revealed that 2h-long exposure to human urine alters MRSA transcriptome, by modifying expression of genes encoding enzymes catalyzing metabolic pathways, virulence factors, and transcriptional regulators. In summary, our results provide important insights into how human urine specifically and rapidly alters MRSA physiology and facilitates MRSA survival in the nutrient-limiting and hostile urinary microenvironment. Importance: Methicillin-resistant Staphylococcus aureus (MRSA) is an uncommon cause of urinary tract infections (UTI) in the general population. However, it is important to understand MRSA pathophysiology in the urinary tract because isolation of MRSA in urine samples often precedes potentially life-threatening MRSA bacteremia. In this report, we describe how exposure to human urine alters MRSA global gene expression and virulence. We hypothesize that these alterations may aid MRSA in acclimating to the nutrient-limiting, immunologically hostile conditions within the urinary tract leading to MRSA-UTI.

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Integrative In Silico and In Vitro Transcriptomics Analysis Revealed Gene Expression Changes and Oncogenic Features of Normal Cholangiocytes after Chronic Alcohol Exposure

International Journal of Molecular Sciences ◽

10.3390/ijms20235987 ◽

2019 ◽

Vol 20 (23) ◽

pp. 5987

Author(s):

Suthipong Chujan ◽

Tawit Suriyo ◽

Jutamaad Satayavivad

Keyword(s):

Gene Expression ◽

Rna Polymerase Ii ◽

Molecular Mechanisms ◽

Function Analysis ◽

Alcohol Exposure ◽

Gene Expression Omnibus ◽

Regulation Of Transcription ◽

Chronic Alcohol ◽

Chronic Alcohol Exposure

Cholangiocarcinoma (CCA) is a malignant tumor originating from cholangiocyte. Prolonged alcohol consumption has been suggested as a possible risk factor for CCA, but there is no information about alcohol’s mechanisms in cholangiocyte. This study was designed to investigate global transcriptional alterations through RNA-sequencing by using chronic alcohol exposure (20 mM for 2 months) in normal human cholangiocyte MMNK-1 cells. To observe the association of alcohol induced CCA pathogenesis, we combined differentially expressed genes (DEGs) with computational bioinformatics of CCA by using publicly gene expression omnibus (GEO) datasets. For biological function analysis, Gene ontology (GO) analysis showed biological process and molecular function related to regulation of transcription from RNA polymerase II promoter, while cellular component linked to the nucleoplasm. KEGG pathway presented pathways in cancer that were significantly enriched. From KEGG result, we further examined the oncogenic features resulting in chronic alcohol exposure, enhanced proliferation, and migration through CCND-1 and MMP-2 up-regulation, respectively. Finally, combined DEGs were validated in clinical data including TCGA and immunohistochemistry from HPA database, demonstrating that FOS up-regulation was related to CCA pathogenesis. This study is the first providing more information and molecular mechanisms about global transcriptome alterations and oncogenic enhancement of chronic alcohol exposure in normal cholangiocytes.

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Overexpression of AtAHL20 causes delayed flowering in Arabidopsis via repression of FT expression

BMC Plant Biology ◽

10.1186/s12870-020-02733-5 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Reuben Tayengwa ◽

Pushpa Sharma Koirala ◽

Courtney F. Pierce ◽

Breanna E. Werner ◽

Michael M. Neff

Keyword(s):

Transgenic Plants ◽

Gene Family ◽

Flowering Time ◽

Camelina Sativa ◽

Negative Regulator ◽

Peptide Sequence ◽

Type I ◽

Mrna Levels ◽

Core Motif ◽

Late Flowering

Abstract Background The 29-member Arabidopsis AHL gene family is classified into three main classes based on nucleotide and protein sequence evolutionary differences. These differences include the presence or absence of introns, type and/or number of conserved AT-hook and PPC domains. AHL gene family members are divided into two phylogenetic clades, Clade-A and Clade-B. A majority of the 29 members remain functionally uncharacterized. Furthermore, the biological significance of the DNA and peptide sequence diversity, observed in the conserved motifs and domains found in the different AHL types, is a subject area that remains largely unexplored. Results Transgenic plants overexpressing AtAHL20 flowered later than the wild type under both short and long days. Transcript accumulation analyses showed that 35S:AtAHL20 plants contained reduced FT, TSF, AGL8 and SPL3 mRNA levels. Similarly, overexpression of AtAHL20’s orthologue in Camelina sativa, Arabidopsis’ closely related Brassicaceae family member species, conferred a late-flowering phenotype via suppression of CsFT expression. However, overexpression of an aberrant AtAHL20 gene harboring a missense mutation in the AT-hook domain’s highly conserved R-G-R core motif abolished the late-flowering phenotype. Data from targeted yeast-two-hybrid assays showed that AtAHL20 interacted with itself and several other Clade-A Type-I AHLs which have been previously implicated in flowering-time regulation: AtAHL19, AtAHL22 and AtAHL29. Conclusion We showed via gain-of-function analysis that AtAHL20 is a negative regulator of FT expression, as well as other downstream flowering time regulating genes. A similar outcome in Camelina sativa transgenic plants overexpressing CsAHL20 suggest that this is a conserved function. Our results demonstrate that AtAHL20 acts as a photoperiod-independent negative regulator of transition to flowering.

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Gene Expression Analysis on the Early Development of Pig Embryos Exposed to Malathion

International Journal of Toxicology ◽

10.1080/10915810701226263 ◽

2007 ◽

Vol 26 (2) ◽

pp. 143-149 ◽

Cited By ~ 4

Author(s):

Zayil Salazar ◽

Yvonne Ducolomb ◽

Miguel Betancourt ◽

Edmundo Bonilla ◽

Leticia Cortés ◽

...

Keyword(s):

Gene Expression ◽

Molecular Mechanisms ◽

Target Genes ◽

Hypothetical Protein ◽

Cdna Libraries ◽

Mhc I ◽

Vitro Fertilization ◽

Embryo Cells ◽

Gene Expression Alterations

Malathion is a widely used pesticide and there is evidence that it could alter mammal’s germ and somatic cells, as well as cell lines. There are not enough studies showing how the nonacute malathion doses affect gene expression. This study analyzes gene expression alterations in pig morular embryos exposed in vitro , for 96 h, to several malathion concentrations after in vitro fertilization. cDNA libraries of isolated morular embryos were created and differential screenings performed to identify target genes. Seven clones were certainly identified. Genes related to mitochondrial metabolism as cytochrome c subunits I and III, nuclear genes such as major histocompatibility complex I (MHC I), and a hypothetical protein related with a splicing factor were the target of malathion’s deregulation effect. The widespread use of malathion as a pesticide should be regarded with reproductive implications and more detailed analysis would yield more about molecular mechanisms of malathion injury on embryo cells.

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Transcriptional signatures throughout development: the effects of mouse embryo manipulation in vitro

Reproduction ◽

10.1530/rep-16-0473 ◽

2017 ◽

Vol 153 (1) ◽

pp. 107-122 ◽

Cited By ~ 15

Author(s):

Sky K Feuer ◽

Xiaowei Liu ◽

Annemarie Donjacour ◽

Rhodel Simbulan ◽

Emin Maltepe ◽

...

Keyword(s):

Gene Expression ◽

Molecular Mechanisms ◽

Preimplantation Embryo ◽

Environmental Exposures ◽

Developmental Time ◽

Transcriptional Responses ◽

Transcriptional Changes ◽

Specific Impact

Stressful environmental exposures incurred early in development can affect postnatal metabolic health and susceptibility to non-communicable diseases in adulthood, although the molecular mechanisms by which this occurs have yet to be elucidated. Here, we use a mouse model to investigate how assortedin vitroexposures restricted exclusively to the preimplantation period affect transcription both acutely in embryos and long term in subsequent offspring adult tissues, to determine if reliable transcriptional markers ofin vitrostress are present at specific developmental time points and throughout development. Eachin vitrofertilization or embryo culture environment led to a specific and unique blastocyst transcriptional profile, but we identified a common 18-gene and 9-pathway signature of preimplantation embryo manipulation that was present in allin vitroembryos irrespective of culture condition or method of fertilization. This fingerprint did not persist throughout development, and there was no clear transcriptional cohesion between adult IVF offspring tissues or compared to their preceding embryos, indicating a tissue-specific impact ofin vitrostress on gene expression. However, the transcriptional changes present in each IVF tissue were targeted by the same upstream transcriptional regulators, which provide insight as to how acute transcriptional responses to stressful environmental exposures might be preserved throughout development to influence adult gene expression.

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Light quality affects the proliferation of in vitro cultured plantlets of Camellia oleifera Huajin

PeerJ ◽

10.7717/peerj.10016 ◽

2020 ◽

Vol 8 ◽

pp. e10016

Author(s):

Chaoyin He ◽

Yanling Zeng ◽

Yuzhong Fu ◽

Jiahao Wu ◽

Qin Liang

Keyword(s):

Tissue Culture ◽

Molecular Mechanisms ◽

Light Quality ◽

Southern China ◽

Stomatal Density ◽

Leaf Shape ◽

Control Treatment ◽

Future Research ◽

Camellia Oleifera

Background Camellia oleifera is an important oil-yielding woody plant native to China. Tea oil extracted from the seeds is rich in health-beneficial compounds. Huajin is a high-yielding elite variety of C. oleifera, with large fruits and remarkable resilience, widely cultivated in southern China; however, its seedling quality tends to be uneven. At present, techniques such as grafting, and cuttings are primarily adopted to propagate C. oleifera. These approaches are susceptible to environmental constraints owing to the long growth period, resulting in the lack of C. oleifera seedlings. Methods to make the cultivation more economical are warranted; this can be facilitated by tissue culture technology to provide good-quality seedlings in a short time. Methods In vitro cultured plantlets of C. oleifera Huajin were exposed to red light (RL), blue light (BL), red:blue light at a 4:1 ratio (R4:B1), and red:blue light at a 1:4 ratio (R1:B4); white light (WL) was used as the control treatment. To investigate the influence of light spectral quality on the proliferation coefficient, photosynthetic pigments, soluble proteins, plant height, leaf shape, Rubisco enzyme activity, and stomata and leaf anatomical features. Results The highest proliferation coefficient was observed under combined red and blue (4:1) light. In addition, this treatment resulted in the second highest chlorophyll content, the thickest palisade and spongy tissues, and consequently, the thickest leaves. The same treatment resulted in the second highest stomatal density, albeit concomitantly with the smallest average stomatal length and width. Discussion These results indicate that high-quality propagation of Huajin shoots can be achieved by culturing the plants in vitro under a combination of red and blue (4:1) lights. Previous studies have shown that red and blue lights improve rooting and transplanting rates of tissue culture seedlings. Hence, future research should focus on the effect of light quality on rooting and transplanting of tissue culture plantlets of Huajin and its specific molecular mechanisms.

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