scholarly journals Light and ripening-regulated BBX protein-encoding genes in Solanum lycopersicum

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Bruno Silvestre Lira ◽  
Maria José Oliveira ◽  
Lumi Shiose ◽  
Raquel Tsu Ay Wu ◽  
Daniele Rosado ◽  
...  
Keyword(s):  
Tomato Fruit ◽  
Protein Family ◽  
Tomato Genome ◽  
Physiological Processes ◽  
Fruit Development And Ripening ◽  
Protein Encoding ◽  
Ripening Inhibitor ◽  
Encoding Genes ◽  
Signalling Cascade

Abstract Light controls several aspects of plant development through a complex signalling cascade. Several B-box domain containing proteins (BBX) were identified as regulators of Arabidopsis thaliana seedling photomorphogenesis. However, the knowledge about the role of this protein family in other physiological processes and species remains scarce. To fill this gap, here BBX protein encoding genes in tomato genome were characterised. The robust phylogeny obtained revealed how the domain diversity in this protein family evolved in Viridiplantae and allowed the precise identification of 31 tomato SlBBX proteins. The mRNA profiling in different organs revealed that SlBBX genes are regulated by light and their transcripts accumulation is directly affected by the chloroplast maturation status in both vegetative and fruit tissues. As tomato fruits develops, three SlBBXs were found to be upregulated in the early stages, controlled by the proper chloroplast differentiation and by the PHYTOCHROME (PHY)-dependent light perception. Upon ripening, other three SlBBXs were transcriptionally induced by RIPENING INHIBITOR master transcriptional factor, as well as by PHY-mediated signalling and proper plastid biogenesis. Altogether, the results obtained revealed a conserved role of SlBBX gene family in the light signalling cascade and identified putative members affecting tomato fruit development and ripening.

scholarly journals The microRNA, miR-133b, functions to slow Duchenne muscular dystrophy pathogenesis

2020 ◽  
Author(s):  
Thomas Taetzsch ◽  
Dillon Shapiro ◽  
Randa Eldosougi ◽  
Tracey Myers ◽  
Robert Settlage ◽  
...  
Keyword(s):  
Duchenne Muscular Dystrophy ◽  
Muscular Dystrophy ◽  
Skeletal Muscles ◽  
Tibialis Anterior Muscle ◽  
Muscle Fibers ◽  
Progressive Degeneration ◽  
Protein Encoding ◽  
Small Muscle ◽  
Encoding Genes

AbstractDuchenne muscular dystrophy (DMD) is characterized by progressive degeneration of skeletal muscles. To date, there are no treatments available to slow or prevent the disease. Hence, it remains essential to identify molecular factors that promote muscle biogenesis since they could serve as therapeutic targets for treating DMD. While the muscle enriched microRNA, miR-133b, has been implicated in the biogenesis of muscle fibers, its role in DMD remains unknown. To assess the role of miR-133b in DMD-affected skeletal muscles, we genetically ablated miR-133b in the mdx mouse model of DMD. In the absence of miR-133b, the tibialis anterior muscle of juvenile and adult mdx mice is populated by small muscle fibers with centralized nuclei, exhibits increased fibrosis, and thickened interstitial space. Additional analysis revealed that loss of miR-133b exacerbates DMD-pathogenesis partly by altering the number of satellite cells and levels of protein-encoding genes, including previously identified miR-133b targets as well as genes involved in cell proliferation and fibrosis. Altogether, our data demonstrate that skeletal muscles utilize miR-133b to mitigate the deleterious effects of DMD.

scholarly journals What Is the Best Lens? Comparing the Resolution Power of Genome-Derived Markers and Standard Barcodes

2021 ◽  
Vol 9 (2) ◽  
pp. 299
Author(s):  
Angela Conti ◽  
Laura Corte ◽  
Debora Casagrande Pierantoni ◽  
Vincent Robert ◽  
Gianluigi Cardinali
Keyword(s):  
Single Copy ◽  
Sensu Stricto ◽  
Fungal Species ◽  
Rrna Genes ◽  
Taxonomic Resolution ◽  
Protein Encoding ◽  
The Many ◽  
Next Generation Sequencing Ngs ◽  
Encoding Genes

Fungal species delimitation was traditionally carried out with multicopy ribosomal RNA (rRNA) genes, principally for their ease of amplification. Since the efficacy of these markers has been questioned, single-copy protein-encoding genes have been proposed alone or in combination for Multi-Locus Sequence Typing (MLST). In this context, the role of the many sequences obtained with Next-Generation Sequencing (NGS) techniques, in both genomics and metagenomics, further pushes toward an analysis of the efficacy of NGS-derived markers and of the metrics to evaluate the marker efficacy in discriminating fungal species. This paper aims at proposing MeTRe (Mean Taxonomic Resolution), a novel index that could be used both for measuring marker efficacy and for assessing the actual resolution (i.e., the level of separation) between species obtained with different markers or their combinations. In this paper, we described and then employed this index to compare the efficacy of two rRNAs and four single-copy markers obtained from public databases as both an amplicon-based approach and genome-derived sequences. Two different groups of species were used, one with a pathogenic species of Candida that was characterized by relatively well-separated taxa, whereas the other, comprising some relevant species of the sensu stricto group of the genus Saccharomyces, included close species and interspecific hybrids. The results showed the ability of MeTRe to evaluate marker efficacy in general and genome-derived markers specifically.

scholarly journals The role of miRNA in regulation of AXL, DAPK1, NFIB gene expression in breast cancer

2018 ◽  
pp. 130-133
Author(s):  
И.В. Пронина ◽  
Е.А. Филиппова ◽  
С.С. Лукина ◽  
А.М. Бурденный ◽  
Т.П. Казубская ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Epithelial Mesenchymal Transition ◽  
Negative Regulator ◽  
Protein Coding ◽  
Mesenchymal Transition ◽  
Protein Encoding ◽  
Apoptotic Pathways ◽  
Encoding Genes

Рак молочной железы (РМЖ) характеризуется эпигенетическими нарушениями, которые приводят к нарушению регуляции экспрессии опухоль ассоциированных белок-кодирующих генов, что влияет на развитие опухоли. Цель исследования - поиск новых микроРНК, потенциально вовлеченных в регуляцию экспрессии 3 белок-кодирующих генов (AXL, DAPK1, NFIB), связанных с регуляцией апоптоза и эпителиально-мезенхимального перехода при РМЖ. Методом количественной ПЦР определены изменения экспрессии 3 белок-кодирующих генов (AXL, DAPK1, NFIB) и 3 микроРНК (miR-127-5p, -132-3р, -9-5p), предсказанных с помощью алгоритмов miRWalk 2.0 как регуляторные. Определены статистически значимые отрицательные корреляции между изменениями уровней экспрессии микроРНК и мРНК для следующих пар: miR-127-5p - DAPK1 (Rs = -0,503, p = 0,001) и miR-9-5p - DAPK1 (Rs = -0,335, p = 0,040). Таким образом, установлена потенциальная роль двух микроРНК в регуляции экспрессии гена DAPK1, активатора различных путей апоптоза и негативного регулятора ЭМП, что имеет фундаментальное значение и может найти применение для разработки таргетной терапии РМЖ. Breast cancer (BC) is characterized by epigenetic disorders, which lead to dysregulation of protein-coding gene expression; together these result in development of a tumor. The goal of the study was to search for new miRNAs that are potentially involved in regulation of the expression of three protein-encoding genes (AXL, DAPK1, NFIB) associated with regulation of apoptosis and the epithelial-mesenchymal transition in breast cancer. Quantitative PCR was used to determine changes in the expression of three protein-coding genes (AXL, DAPK1, NFIB) and three miRNAs (miR-127-5p, -132-3p, -9-5p) that had been predicted to be regulators by miRWalk 2.0 algorithms. Statistically significant negative correlations between changes in miRNA and mRNA expression were determined for the following pairs: miR-127-5p - DAPK1 (Rs = -0.503, p = 0.001) and miR-9-5p - DAPK1 (Rs = -0.335, p = 0.040). Therefore, the study showed a potential role of two miRNAs in regulation of the DAPK1 gene expression, an activator of various apoptotic pathways and a negative regulator of EMT. This result is fundamentally important and can be used to develop targeted therapies for breast cancer.

scholarly journals 736 PB 032 5-AMINOLEVULINIC ACID DEHYDRATASE ACTIVITY DURING TOMATO FRUIT DEVELOPMENT AND RIPENING

HortScience ◽  
1994 ◽  
Vol 29 (5) ◽  
pp. 538d-538
Author(s):  
Marios C. Kyriacou ◽  
David J. Hannapel ◽  
Richard J. Gladon
Keyword(s):  
Aminolevulinic Acid ◽  
Developmental Regulation ◽  
Chlorophyll Biosynthesis ◽  
Tomato Fruit ◽  
Assay Procedure ◽  
Tomato Fruit Ripening ◽  
Fruit Development And Ripening ◽  
Alad Activity ◽  
Dehydratase Activity

Tomato fruit ripening is characterized by a decrease in chlorophyll content and an increase in lycopene synthesis. 5-Aminolevulinic acid (ALA) dehydratase (ALAD) is the fruit committed enzyme in the chlorophyll and heme biosynthetic pathways, and it catalyzes the dimerization of two ALA molecules into porphobilinogen We have focused our attention on the potential pivotal role of ALAD in the developmental regulation of chlorophyll biosynthesis during tomato fruit growth, development, and ripening. We have standardized an assay procedure for measuring the enzymatic activity of ALAD in tomato fruit tissues. The activity of ALAD was assayed from ten days past anthesis to day 60, when fruits where void of chlorophyll. We observed a several-fold decline in ALAD activity to residual levels during fruit ontogeny. Our data also show greater ALAD activity in chlorophyllous organs (leaves, stems, immature fruits) than in nonchlorophyllous organs (roots, ripe fruits), where heme production is predominant.

scholarly journals Identification and Expression Analysis of Hormone Biosynthetic and Metabolism Genes in the 2OGD Family for Identifying Genes That May Be Involved in Tomato Fruit Ripening

2020 ◽  
Vol 21 (15) ◽  
pp. 5344
Author(s):  
Qiangqiang Ding ◽  
Feng Wang ◽  
Juan Xue ◽  
Xinxin Yang ◽  
Junmiao Fan ◽  
...  
Keyword(s):  
Acetic Acid ◽  
Fruit Ripening ◽  
Fruit Development ◽  
Tomato Fruit ◽  
Protein Family ◽  
Protein Families ◽  
Tomato Fruit Ripening ◽  
Fruit Development And Ripening ◽  
Hormone Biosynthesis ◽  
Indole 3 Acetic Acid

Phytohormones play important roles in modulating tomato fruit development and ripening. The 2-oxoglutarate-dependent dioxygenase (2OGD) superfamily containing several subfamilies involved in hormone biosynthesis and metabolism. In this study, we aimed to identify hormone biosynthesis and metabolism-related to 2OGD proteins in tomato and explored their roles in fruit development and ripening. We identified nine 2OGD protein subfamilies involved in hormone biosynthesis and metabolism, including the gibberellin (GA) biosynthetic protein families GA20ox and GA3ox, GA degradation protein families C19-GA2ox and C20-GA2ox, ethylene biosynthetic protein family ACO, auxin degradation protein family DAO, jasmonate hydroxylation protein family JOX, salicylic acid degradation protein family DMR6, and strigolactone biosynthetic protein family LBO. These genes were differentially expressed in different tomato organs. The GA degradation gene SlGA2ox2, and the auxin degradation gene SlDAO1, showed significantly increased expression from the mature-green to the breaker stage during tomato fruit ripening, accompanied by decreased endogenous GA and auxin, indicating that SlGA2ox2 and SlDAO1 were responsible for the reduced GA and auxin concentrations. Additionally, exogenous gibberellin 3 (GA3) and indole-3-acetic acid (IAA) treatment of mature-green fruits delayed fruit ripening and increased the expression of SlGA2ox2 and SlDAO1, respectively. Therefore, SlGA2ox2 and SlDAO1 are implicated in the degradation of GAs and auxin during tomato fruit ripening.

Expression study of soybean germin-like gene family reveals a role of GLP7 gene in various abiotic stress tolerances

2016 ◽  
Vol 96 (2) ◽  
pp. 296-304 ◽  
Author(s):  
Yongguang Li ◽  
Dayong Zhang ◽  
Weina Li ◽  
Ali Inayat Mallano ◽  
Yuhang Zhang ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Responses ◽  
Primary Root ◽  
Plant Glycoproteins ◽  
Protein Encoding ◽  
Oxidative Tolerance ◽  
Abiotic Stress Treatment ◽  
Encoding Genes ◽  
Soybean Leave

Germin-like proteins (GLPs) are ubiquitous plant glycoproteins (belonging to the cupin super family) that play diverse roles, including abiotic stress resistance in many plant species. To identify the molecular functions underlying abiotic stress responses, the expression of germin-like protein encoding genes of soybean GmGLPs was analyzed. qRT-PCR analyses of 21 GmGLPs transcripts abundances were conducted in soybean leave tissues. The results showed that GmGLPs transcripts were highly abundant upon treatments with high salinity, PEG6000, abscisic acid (ABA) and methyl viologen (MV). The peaks of transcript copiousness induced by PEG6000 and NaCl were mostly observed after 18 h, while some genes expressed earlier than 4 h after abiotic stress treatment. A specific GmGLP7 gene, that was highly abundant under salinity, drought, ABA and MV conditions, was further characterized. The ectopic overexpression of GmGLP7 (Glyma.08G226800.1) in transgenic Arabidopsis enhanced drought, salt, and oxidative tolerance and resulted in hypersensitive phenotypes toward ABA-mediated seed germination and primary root elongation, compared to the wild-type. Taken together, these results suggest that GmGLP7 positively confers abiotic tolerance in plants.

scholarly journals RNA Arbitrarily Primed PCR Survey of Genes Regulated by ToxR in the Deep-Sea Bacterium Photobacterium profundum Strain SS9

2001 ◽  
Vol 183 (5) ◽  
pp. 1688-1693 ◽  
Author(s):  
Kelly A. Bidle ◽  
Douglas H. Bartlett
Keyword(s):  
Gene Expression ◽  
Virulence Gene ◽  
Environmental Signals ◽  
Virulence Gene Expression ◽  
New Genes ◽  
Protein Encoding ◽  
Arbitrarily Primed Pcr ◽  
Photobacterium Profundum ◽  
Encoding Genes

ABSTRACT We are currently investigating the role of ToxR-mediated gene regulation in Photobacterium profundum strain SS9. SS9 is a moderately piezophilic (“pressure loving”) psychrotolerant marine bacterium belonging to the family Vibrionaceae. InVibrio cholerae, ToxR is a transmembrane DNA binding protein involved in mediating virulence gene expression in response to various environmental signals. A homolog to V. choleraeToxR that is necessary for pressure-responsive gene expression of two outer membrane protein-encoding genes was previously found in SS9. To search for additional genes regulated by ToxR in SS9, we have used RNA arbitrarily primed PCR (RAP-PCR) with wild-type and toxRmutant strains of SS9. Seven ToxR-activated transcripts and one ToxR-repressed transcript were identified in this analysis. The cDNAs corresponding to these partial transcripts were cloned and sequenced, and ToxR regulation of their genes was verified. The products of these genes are all predicted to fall into one or both of two functional categories, those whose products alter membrane structure and/or those that are part of a starvation response. The transcript levels of all eight newly identified genes were also characterized as a function of hydrostatic pressure. Various patterns of pressure regulation were observed, indicating that ToxR activation or repression cannot be used to predict the influence of pressure on gene expression in SS9. These results provide further information on the nature of the ToxR regulon in SS9 and indicate that RAP-PCR is a useful approach for the discovery of new genes under the control of global regulatory transcription factors.

scholarly journals A tomato LATERAL ORGAN BOUNDARIES transcription factor, SlLOB1, predominantly regulates cell wall and softening components of ripening

2021 ◽  
Vol 118 (33) ◽  
pp. e2102486118
Author(s):  
Yanna Shi ◽  
Julia Vrebalov ◽  
Hui Zheng ◽  
Yimin Xu ◽  
Xueren Yin ◽  
...  
Keyword(s):  
Cell Wall ◽  
Tomato Fruit ◽  
35S Promoter ◽  
Protein Levels ◽  
Physiological Processes ◽  
Tomato Fruit Ripening ◽  
Lateral Organ ◽  
Textural Changes ◽  
Late Maturation

Fruit softening is a key component of the irreversible ripening program, contributing to the palatability necessary for frugivore-mediated seed dispersal. The underlying textural changes are complex and result from cell wall remodeling and changes in both cell adhesion and turgor. While a number of transcription factors (TFs) that regulate ripening have been identified, these affect most canonical ripening-related physiological processes. Here, we show that a tomato fruit ripening–specific LATERAL ORGAN BOUNDRIES (LOB) TF, SlLOB1, up-regulates a suite of cell wall–associated genes during late maturation and ripening of locule and pericarp tissues. SlLOB1 repression in transgenic fruit impedes softening, while overexpression throughout the plant under the direction of the 35s promoter confers precocious induction of cell wall gene expression and premature softening. Transcript and protein levels of the wall-loosening protein EXPANSIN1 (EXP1) are strongly suppressed in SlLOB1 RNA interference lines, while EXP1 is induced in SlLOB1-overexpressing transgenic leaves and fruit. In contrast to the role of ethylene and previously characterized ripening TFs, which are comprehensive facilitators of ripening phenomena including softening, SlLOB1 participates in a regulatory subcircuit predominant to cell wall dynamics and softening.

scholarly journals Comprehensive Analysis of Arabinogalactan Protein-Encoding Genes Reveals the Involvement of Three BrFLA Genes in Pollen Germination in Brassica rapa

2021 ◽  
Vol 22 (23) ◽  
pp. 13142
Author(s):  
Huiting Huang ◽  
Yingjing Miao ◽  
Yuting Zhang ◽  
Li Huang ◽  
Jiashu Cao ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Pollen Germination ◽  
Protein Structures ◽  
Pollen Grains ◽  
Comprehensive Analysis ◽  
Arabinogalactan Protein ◽  
Sequencing Data ◽  
Protein Encoding ◽  
Encoding Genes

Arabinogalactan proteins (AGPs) are a superfamily of hydroxyproline-rich glycoproteins that are massively glycosylated, widely implicated in plant growth and development. No comprehensive analysis of the AGP gene family has been performed in Chinese cabbage (Brassica rapa ssp. chinensis). Here, we identified a total of 293 putative AGP-encoding genes in B. rapa, including 25 classical AGPs, three lysine-rich AGPs, 30 AG-peptides, 36 fasciclin-like AGPs (FLAs), 59 phytocyanin-like AGPs, 33 xylogen-like AGPs, 102 other chimeric AGPs, two non-classical AGPs and three AGP/extensin hybrids. Their protein structures, phylogenetic relationships, chromosomal location and gene duplication status were comprehensively analyzed. Based on RNA sequencing data, we found that 73 AGP genes were differentially expressed in the floral buds of the sterile and fertile plants at least at one developmental stage in B. rapa, suggesting a potential role of AGPs in male reproductive development. We further characterized BrFLA2, BrFLA28 and BrFLA32, three FLA members especially expressed in anthers, pollen grains and pollen tubes. BrFLA2, BrFLA28 and BrFLA32 are indispensable for the proper timing of pollen germination under high relative humidity. Our study greatly extends the repertoire of AGPs in B. rapa and reveals a role for three members of the FLA subfamily in pollen germination.

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