scholarly journals Regulation of dhurrin pathway gene expression during Sorghum bicolor development

Planta ◽  
2021 ◽  
Vol 254 (6) ◽  
Author(s):  
Roslyn M. Gleadow ◽  
Brian A. McKinley ◽  
Cecilia K. Blomstedt ◽  
Austin C. Lamb ◽  
Birger Lindberg Møller ◽  
...  
Keyword(s):  
Gene Expression ◽  
Sorghum Bicolor ◽  
Expression Patterns ◽  
Plant Defence ◽  
Grain Filling ◽  
Specific Expression ◽  
Expression Of Genes ◽  
Pathway Gene ◽  
Organ Specific ◽  
Organ Specific Expression

Abstract Main conclusion Developmental and organ-specific expression of genes in dhurrin biosynthesis, bio-activation, and recycling offers dynamic metabolic responses optimizing growth and defence responses in Sorghum. Abstract Plant defence models evaluate the costs and benefits of resource investments at different stages in the life cycle. Poor understanding of the molecular regulation of defence deployment and remobilization hampers accuracy of the predictions. Cyanogenic glucosides, such as dhurrin are phytoanticipins that release hydrogen cyanide upon bio-activation. In this study, RNA-seq was used to investigate the expression of genes involved in the biosynthesis, bio-activation and recycling of dhurrin in Sorghum bicolor. Genes involved in dhurrin biosynthesis were highly expressed in all young developing vegetative tissues (leaves, leaf sheath, roots, stems), tiller buds and imbibing seeds and showed gene specific peaks of expression in leaves during diel cycles. Genes involved in dhurrin bio-activation were expressed early in organ development with organ-specific expression patterns. Genes involved in recycling were expressed at similar levels in the different organ during development, although post-floral initiation when nutrients are remobilized for grain filling, expression of GSTL1 decreased > tenfold in leaves and NITB2 increased > tenfold in stems. Results are consistent with the establishment of a pre-emptive defence in young tissues and regulated recycling related to organ senescence and increased demand for nitrogen during grain filling. This detailed characterization of the transcriptional regulation of dhurrin biosynthesis, bioactivation and remobilization genes during organ and plant development will aid elucidation of gene regulatory networks and signalling pathways that modulate gene expression and dhurrin levels. In-depth knowledge of dhurrin metabolism could improve the yield, nitrogen use efficiency and stress resilience of Sorghum.

scholarly journals Impact of IL-1 signalling on experimental uveitis and arthritis

2012 ◽  
Vol 71 (5) ◽  
pp. 753-760 ◽  
Author(s):  
Stephen R Planck ◽  
April Woods ◽  
Jenna S Clowers ◽  
Martin J Nicklin ◽  
James T Rosenbaum ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Eye Disease ◽  
Negative Regulators ◽  
Specific Expression ◽  
Local Responses ◽  
Intraocular Injection ◽  
Inflammatory Eye Disease ◽  
Pathogenesis Related ◽  
Organ Specific ◽  
Organ Specific Expression

BackgroundUveitis, or inflammatory eye disease, is a common extra-articular manifestation of many systemic autoinflammatory diseases involving the joints. Anakinra (recombinant interleukin (IL)-1 receptor antagonist (Ra)) is an effective therapy in several arthritic diseases; yet, few studies have investigated the extent to which IL-1 signalling or IL-1Ra influences the onset and/or severity of uveitis.ObjectiveTo seek possible links between arthritis and uveitis pathogenesis related to IL-1 signalling.MethodsThe eyes of IL-1Ra-deficient BALB/c mice were monitored histologically and by intravital videomicroscopy to determine if uveitis developed along with the expected spontaneous arthritis in ankles and knees. Expression levels of IL-1R and its negative regulators (IL-1Ra, IL-1RII, IL-1RAcP and single Ig IL-1R-related molecule) in eye and joint tissues were compared. Differences in uveitis induced by intraocular injection of lipopolysaccharide (LPS) in mice lacking IL-1R or IL-1Ra were assessed.ResultsDeficiency in IL-1Ra predisposes to spontaneous arthritis, which is exacerbated by previous systemic LPS exposure. The eye, however, does not develop inflammatory disease despite the progressive arthritis or LPS exposure. Organ-specific expression patterns for IL-1Ra and negative regulators of IL-1 activity were observed that appear to predict predisposition to inflammation in each location in IL-1Ra knockout mice. The eye is extremely sensitive to locally administered LPS, and IL-1Ra deficiency markedly exacerbates the resulting uveitis.ConclusionThis study demonstrates that IL-1Ra plays an important role in suppressing local responses in eyes injected with LPS and that there is discordance between murine eyes and joints in the extent to which IL-1Ra protects against spontaneous inflammation.

Expression analysis of seed-specific genes in four angiosperm species with an emphasis on the unconserved expression patterns of homologous genes

2013 ◽  
Vol 23 (4) ◽  
pp. 223-231 ◽  
Author(s):  
Lichao Ma ◽  
Yanrong Wang ◽  
Wenxian Liu ◽  
Zhipeng Liu
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Homologous Gene ◽  
Promoter Regions ◽  
Specific Expression ◽  
Seed Formation ◽  
Control Seed ◽  
Homologous Genes ◽  
Expression Of Genes ◽  
Angiosperm Species

AbstractMedicago truncatula, soybean (Glycine max), Arabidopsis thaliana and rice (Oryza sativa) all belong to the core angiosperm group of plants. Seed-specific genes are important for seed formation and development in these angiosperms. The identification of genes specifically expressed in angiosperm seeds and the comparison of the expression patterns of homologous genes among different angiosperm species can provide novel insights into the functions of genes that control seed development and the evolution of angiosperms. We downloaded the sequences and expression data from the relevant databases, and the seed-specific expression of genes was identified with cut-offs of a gene expression level ratio ≥ 5 and a Z-score ≥ 6. The genes were analysed using local BLAST software with an E-value ≤ 1.0E − 505. A total of 605, 581, 778 and 722 genes showed specific expression in the seeds of Medicago, soybean, Arabidopsis and rice, respectively. Additionally, we compared the expression patterns of seed-specific genes from each species with their homologues in the other three species, and found that the degree of variation in the expression patterns of homologous genes was low among closely related species but higher among more distantly related ones. The discrepancy between the homologous gene expression patterns may be caused by the different characteristics of the cis-elements in the promoter regions of the homologous genes.

scholarly journals A common molecular basis to the convergent evolution of the selfing syndrome in Capsella

2019 ◽  
Author(s):  
Natalia Joanna Woźniak ◽  
Christian Kappel ◽  
Cindy Marona ◽  
Lothar Altschmied ◽  
Barbara Neuffer ◽  
...  
Keyword(s):  
Convergent Evolution ◽  
Evolutionary Biology ◽  
Expression Patterns ◽  
Network Connectivity ◽  
Specific Expression ◽  
Organ Specific ◽  
Self Fertilization ◽  
Organ Specific Expression ◽  
Comparative Genetic Mapping ◽  
Selfing Syndrome

AbstractWhether, and to what extent, phenotypic evolution follows predictable genetic paths, remains an important question in evolutionary biology. Convergent evolution of similar characters provides a unique opportunity to address this question. The transition to selfing and the associated changes in flower morphology are among the most prominent examples of repeated evolution in plants. Yet, to date no studies have directly compared the extent of similarities between convergent adaptations to selfing. In this study, we take advantage of the independent transitions to self-fertilization in the genus Capsella to test the existence of genetic and developmental constraints imposed on flower evolution in the context of the selfing syndrome. While C. rubella and C. orientalis have emerged independently, both have evolved almost identical flower characters. Not only the evolutionary outcome is identical but, in both cases, the same developmental strategies underlie the convergent reduction of flower size. This has been associated with convergent evolution of gene-expression changes. The transcriptomic changes common to both selfing lineages are enriched in genes with low-network connectivity and with organ-specific expression patterns. Comparative genetic mapping also indicates that, at least in the case of petal size evolution, these similarities are largely caused by mutations at the same loci. Together, these results suggest that the limited availability of low-pleiotropy paths predetermine closely related species to similar evolutionary outcomes.

scholarly journals Genome-Wide Identification and Expression Profiling of the BZR Transcription Factor Gene Family in Nicotiana benthamiana

2021 ◽  
Vol 22 (19) ◽  
pp. 10379
Author(s):  
Xuwei Chen ◽  
Xinyang Wu ◽  
Shiyou Qiu ◽  
Hongying Zheng ◽  
Yuwen Lu ◽  
...  
Keyword(s):  
Stress Resistance ◽  
Nicotiana Benthamiana ◽  
Expression Patterns ◽  
Basic Research ◽  
Drought Treatment ◽  
Specific Expression ◽  
Cis Acting ◽  
Genome Wide ◽  
Organ Specific ◽  
Organ Specific Expression

Brassinazole-resistant (BZR) family genes encode plant-specific transcription factors (TFs), play essential roles in the regulation of plant growth and development, and have multiple stress-resistance functions. Nicotiana benthamiana is a model plant widely used in basic research. However, members of the BZR family in N. benthamiana have not been identified, and little is known about their function in abiotic stress. In this study, a total of 14 BZR members were identified in the N. benthamiana genome, which could be divided into four groups according to a phylogenetic tree. NbBZRs have similar exon-intron structures and conserved motifs, and may be regulated by cis-acting elements such as STRE, TCA, and ARE, etc. Organ-specific expression analysis showed that NbBZR members have different and diverse expression patterns in different tissues, and most of the members are expressed in roots, stems, and leaves. The analysis of the expression patterns in response to different abiotic stresses showed that all the tested NbBZR members showed a significant down-regulation after drought treatment. Many NbBZR genes also responded in various ways to cold, heat and salt stress treatments. The results imply that NbBZRs have multiple functions related to stress resistance.

Mass-Spectrometry-Based Proteomics Reveals Organ-Specific Expression Patterns To Be Used as Forensic Evidence

2015 ◽  
Vol 15 (1) ◽  
pp. 182-192 ◽  
Author(s):  
Sascha Dammeier ◽  
Sven Nahnsen ◽  
Johannes Veit ◽  
Frank Wehner ◽  
Marius Ueffing ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Expression Patterns ◽  
Forensic Evidence ◽  
Specific Expression ◽  
Organ Specific ◽  
Organ Specific Expression

scholarly journals Circular RNAs: characteristics, biogenesis, mechanisms and functions in liver cancer

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Hao Shen ◽  
Boqiang Liu ◽  
Junjie Xu ◽  
Bin Zhang ◽  
Yifan Wang ◽  
...  
Keyword(s):  
Liver Cancer ◽  
Drug Targets ◽  
Rna Binding ◽  
Expression Patterns ◽  
Circular Rnas ◽  
Specific Expression ◽  
Treatment Regimens ◽  
Organ Specific ◽  
Transcription Regulators ◽  
Organ Specific Expression

Abstract Background Hepatocellular carcinoma (HCC) is one of the most common malignancies globally. Despite aggressive and multimodal treatment regimens, the overall survival of HCC patients remains poor. Main Circular RNAs (circRNAs) are noncoding RNAs (ncRNAs) with covalently closed structures and tissue- or organ-specific expression patterns in eukaryotes. They are highly stable and have important biological functions, including acting as microRNA sponges, protein scaffolds, transcription regulators, translation templates and interacting with RNA-binding protein. Recent advances have indicated that circRNAs present abnormal expression in HCC tissues and that their dysregulation contributes to HCC initiation and progression. Furthermore, researchers have revealed that some circRNAs might serve as diagnostic biomarkers or drug targets in clinical settings. In this review, we systematically evaluate the characteristics, biogenesis, mechanisms and functions of circRNAs in HCC and further discuss the current shortcomings and potential directions of prospective studies on liver cancer-related circRNAs. Conclusion CircRNAs are a novel class of ncRNAs that play a significant role in HCC initiation and progression, but their internal mechanisms and clinical applications need further investigation.

scholarly journals Integrating metabolomics and targeted gene expression to uncover potential biomarkers of fungal/oomycetes-associated disease susceptibility in grapevine

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Marisa Maia ◽  
António E. N. Ferreira ◽  
Rui Nascimento ◽  
Filipa Monteiro ◽  
Francisco Traquete ◽  
...  
Keyword(s):  
Gene Expression ◽  
Plant Defence ◽  
Breeding Programs ◽  
Analysis Group ◽  
Expression Of Genes ◽  
Leucoanthocyanidin Reductase ◽  
Defence Responses ◽  
Targeted Gene Expression ◽  
Plant Defence Responses ◽  
First Time

Abstract Vitis vinifera, one of the most cultivated fruit crops, is susceptible to several diseases particularly caused by fungus and oomycete pathogens. In contrast, other Vitis species (American, Asian) display different degrees of tolerance/resistance to these pathogens, being widely used in breeding programs to introgress resistance traits in elite V. vinifera cultivars. Secondary metabolites are important players in plant defence responses. Therefore, the characterization of the metabolic profiles associated with disease resistance and susceptibility traits in grapevine is a promising approach to identify trait-related biomarkers. In this work, the leaf metabolic composition of eleven Vitis genotypes was analysed using an untargeted metabolomics approach. A total of 190 putative metabolites were found to discriminate resistant/partial resistant from susceptible genotypes. The biological relevance of discriminative compounds was assessed by pathway analysis. Several compounds were selected as promising biomarkers and the expression of genes coding for enzymes associated with their metabolic pathways was analysed. Reference genes for these grapevine genotypes were established for normalisation of candidate gene expression. The leucoanthocyanidin reductase 2 gene (LAR2) presented a significant increase of expression in susceptible genotypes, in accordance with catechin accumulation in this analysis group. Up to our knowledge this is the first time that metabolic constitutive biomarkers are proposed, opening new insights into plant selection on breeding programs.

scholarly journals Genome Wide Analysis of the Transcriptional Profiles in Different Regions of the Developing Rice Grains

Rice ◽  
2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Ting-Ying Wu ◽  
Marlen Müller ◽  
Wilhelm Gruissem ◽  
Navreet K. Bhullar
Keyword(s):  
Gene Expression ◽  
Dna Sequence ◽  
Expression Patterns ◽  
Grain Filling ◽  
Aleurone Layer ◽  
Rice Grain ◽  
Sequence Motifs ◽  
Grain Development ◽  
Spatio Temporal ◽  
Dna Sequence Motifs

Abstract Background Rice is an important food source for humans worldwide. Because of its nutritional and agricultural significance, a number of studies addressed various aspects of rice grain development and grain filling. Nevertheless, the molecular processes underlying grain filling and development, and in particular the contributions of different grain tissues to these processes, are not understood. Main Text Using RNA-sequencing, we profiled gene expression activity in grain tissues comprised of cross cells (CC), the nucellar epidermis (NE), ovular vascular trace (OVT), endosperm (EN) and the aleurone layer (AL). These tissues were dissected using laser capture microdissection (LCM) at three distinct grain development stages. The mRNA expression datasets offer comprehensive and new insights into the gene expression patterns in different rice grain tissues and their contributions to grain development. Comparative analysis of the different tissues revealed their similar and/or unique functions, as well as the spatio-temporal regulation of common and tissue-specific genes. The expression patterns of genes encoding hormones and transporters indicate an important role of the OVT tissue in metabolite transport during grain development. Gene co-expression network prediction on OVT-specific genes identified several distinct and common development-specific transcription factors. Further analysis of enriched DNA sequence motifs proximal to OVT-specific genes revealed known and novel DNA sequence motifs relevant to rice grain development. Conclusion Together, the dataset of gene expression in rice grain tissues is a novel and useful resource for further work to dissect the molecular and metabolic processes during rice grain development.

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