Transcriptome profiling of postharvest shoots identifies PheNAP2- and PheNAP3-promoted shoot senescence

2019 ◽  
Vol 39 (12) ◽  
pp. 2027-2044 ◽  
Author(s):  
Xiangyu Li ◽  
Lihua Xie ◽  
Huifang Zheng ◽  
Miaomiao Cai ◽  
Zhanchao Cheng ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Leucine Zipper ◽  
Molecular Mechanisms ◽  
Normal Growth ◽  
Transcriptome Profiling ◽  
Cellular Division ◽  
Stay Green ◽  
Nac Transcription Factors ◽  
Helix Loop Helix ◽  
Postharvest Senescence

Abstract The juvenile shoots of Phyllostachys edulis have been used as a food source for thousands of years, and it is recognized as a potential source of nutraceuticals. However, its rapid senescence restricts bamboo production and consumption, and the underlying molecular mechanisms of rapid shoot senescence remain largely unclear. In the present study, transcriptome profiling was employed to investigate the molecular regulation of postharvest senescence in shoots, along with physiological assays and anatomical dissections. Results revealed a distinct shift in expression postharvest, specifically transitions from cellular division and differentiation to the relocation of nutrients and programmed cell death. A number of regulatory and signaling factors were induced during postharvest senescence. Moreover, transcription factors, including NAM, ATAF and CUC (NAC) transcription factors, basic helix–loop–helix transcription factors, basic region/leucine zipper transcription factors, MYB transcription factors and WRKY transcription factors, were critical for shoot postharvest senescence, of which NACs were the most abundant. PheNAP2 and PheNAP3 were induced in postharvest shoots and found to promote leaf senescence in Arabidopsis by inducing the expression of AtSAG12 and AtSAG113. PheNAP2 and PheNAP3 could both restore the stay-green Arabidopsis nap to the wild-type phenotype either under normal growth condition or under abscisic acid treatment. Collectively, these results suggest that PheNAPs may promote shoot senescence. These findings provide a systematic view of shoot senescence and will inform future studies on the underlying molecular mechanisms responsible for shoot degradation during storage.

scholarly journals Transcriptome profiling reveals the effects of drought tolerance in Giant Juncao

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jing Zhou ◽  
Siqi Chen ◽  
Wenjiao Shi ◽  
Rakefet David-Schwartz ◽  
Sutao Li ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Leucine Zipper ◽  
Molecular Mechanisms ◽  
Normal Growth ◽  
Transcriptome Profiling ◽  
Fatty Acyl ◽  
Transferase Activity ◽  
Forage Production ◽  
Basic Leucine Zipper

Abstract Background Giant Juncao is often used as feed for livestock because of its huge biomass. However, drought stress reduces forage production by affecting the normal growth and development of plants. Therefore, investigating the molecular mechanisms of drought tolerance will provide important information for the improvement of drought tolerance in this grass. Results A total of 144.96 Gb of clean data was generated and assembled into 144,806 transcripts and 93,907 unigenes. After 7 and 14 days of drought stress, a total of 16,726 and 46,492 differentially expressed genes (DEGs) were observed, respectively. Compared with normal irrigation, 16,247, 23,503, and 11,598 DEGs were observed in 1, 5, and 9 days following rehydration, respectively. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed abiotic stress-responsive genes and pathways related to catalytic activity, methyltransferase activity, transferase activity, and superoxide metabolic process. We also identified transcription factors belonging to several families, including basic helix-loop-helix (bHLH), WRKY, NAM (no apical meristem), ATAF1/2 and CUC2 (cup-shaped cotyledon) (NAC), fatty acyl-CoA reductase (FAR1), B3, myeloblastosis (MYB)-related, and basic leucine zipper (bZIP) families, which are important drought-rehydration-responsive proteins. Weighted gene co-expression network analysis was also used to analyze the RNA-seq data to predict the interrelationship between genes. Twenty modules were obtained, and four of these modules may be involved in photosynthesis and plant hormone signal transduction that respond to drought and rehydration conditions. Conclusions Our research is the first to provide a more comprehensive understanding of DEGs involved in drought stress at the transcriptome level in Giant Juncao with different drought and recovery conditions. These results may reveal insights into the molecular mechanisms of drought tolerance in Giant Juncao and provide diverse genetic resources involved in drought tolerance research.

scholarly journals Physiological and Transcriptomic Responses to Nitrogen Deficiency in Neolamarckia cadamba

2021 ◽  
Vol 12 ◽  
Author(s):  
Lu Lu ◽  
Yuanyuan Zhang ◽  
Lu Li ◽  
Na Yi ◽  
Yi Liu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Leucine Zipper ◽  
Molecular Mechanisms ◽  
Lignin Content ◽  
Nitrogen Deficiency ◽  
Essential Elements ◽  
Ammonium Transporter ◽  
Basic Leucine Zipper ◽  
Transporter Protein ◽  
Helix Loop Helix

Nitrogen (N) is one of the abundant and essential elements for plant growth and development, and N deficiency (ND) affects plants at both physiological and transcriptomic levels. Neolamarckia cadamba is a fast-growing woody plant from the Rubiaceae family. However, the physiological and molecular impacts of ND on this species have not been well investigated. Here, we studied how N. cadamba responds to ND under hydroponic conditions. In a physiological aspect, ND led to a reduction in biomass, chlorophyll content, and photosynthetic capacity. ND also impaired the assimilation of N as the activities of glutamine synthetase (GS) and nitrate reductase (NR) were decreased in the root. Interestingly, the lignin content of stem increased progressively during the ND stress. The main transcription factors, the transcription factors that are important to N regulation has been found to be upregulated, including Nodule inception-like protein 7 (NLP7), TGACG motif-binding factor 1 (TGA1), basic helix-loop-helix protein 45 (BHLH45), NAM, ATAF1,2, CUC2 (NAC) transcription factor 43 (NAC43), and basic leucine zipper pattern 44 (bZIP44). The expression of N transporters, such as nitrate transporter 2.4 (NRT2.4), ammonium transporter 3 (AMT3), and amino acid transporter protein 3 (AAP3), was also upregulated. In addition, phosphorus- and calcium-related genes such as phosphate starvation response 2 (PHR2) and cyclic nucleotide-gated ion channel 15 (CNGC15) were expressed more abundantly in response to ND stress. Our results reveal the physiological and molecular mechanisms by which woody plants respond to ND.

scholarly journals An evolutionarily conserved leucine zipper-like motif accounts for strong tetramerization capabilities of SEPALLATA-like MADS-domain transcription factors controlling flower development

2017 ◽  
Author(s):  
Florian Rümpler ◽  
Günter Theißen ◽  
Rainer Melzer
Keyword(s):  
Transcription Factors ◽  
Amino Acid ◽  
Flower Development ◽  
Leucine Zipper ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Specific Interaction ◽  
Angiosperm Evolution ◽  
Protein Protein Interaction ◽  
Organ Specific

ABSTRACTThe development of angiosperm flowers is regulated by homeotic MIKC-type MADS-domain transcription factors that activate or repress target genes via the formation of DNA-bound, organ specific tetrameric complexes. The protein-protein interaction (PPI) capabilities differ considerably between different MIKC-type proteins. The floral homeotic protein SEPALLATA3 (SEP3) acts as a hub that incorporates numerous other MADS-domain proteins into tetrameric complexes that would otherwise not form. However, the molecular mechanisms that underlie these promiscuous interactions remain largely unknown. In this study we created a collection of amino acid substitution mutants of SEP3 to quantify the contribution of individual residues on protein tetramerization during DNA-binding, employing methods of molecular biophysics. We show that leucine residues at certain key positions form a leucine zipper structure that is essential for tetramerization of SEP3, whereas the introduction of physicochemically very similar residues at respective sites impedes the formation of DNA-bound tetramers. Comprehensive molecular evolutionary analyses of MADS-domain proteins from a diverse set of flowering plants revealed exceedingly high conservation of the identified leucine residues within SEP3-subfamily proteins throughout angiosperm evolution. In contrast, MADS-domain proteins that are unable to tetramerize among themselves exhibit preferences for other amino acids at homologous sites. Our findings indicate that the subfamily-specific conservation of amino acid residues at just a few key positions account for subfamily-specific interaction capabilities of MADS-domain transcription factors and shaped the present-day structure of the PPI network controlling flower development.

scholarly journals Transcriptome analysis of immature xylem in Chinese fir at different developmental phases

2016 ◽  
Author(s):  
Yunxing Zhang ◽  
Xiaojiao Han ◽  
Jian Sang ◽  
Xuelian he ◽  
Mingying Liu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Transcriptome Sequencing ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Southern China ◽  
Wood Formation ◽  
Chinese Fir ◽  
Nac Transcription Factors ◽  
Transcriptome Variation ◽  
Developmental Phases

Background: Chinese fir [Cunninghamia lanceolata (Lamb .) Hook.], is one of the most important native tree species for timber production in southern China. An understanding of overall fast growing stage, stem growth stage and senescence stage cambium transcriptome variation is lacking. We used transcriptome sequencing to identify the repertoire of genes expressed during development of xylem tissue in Chinese fir, aiming to delineate the molecular mechanisms of wood formation. Results: We carried out transcriptome sequencing at three different cultivation ages (7Y, 15Y and 21Y) generating 68.71 million reads (13.88 Gbp). A total of 140,486 unigenes with a mean size of 568.64 base pairs (bp) were obtained via de novo assembly. Of these, 27,427 unigenes (19.52%) were further annotated by comparison to public protein databases. A total of 5,331 (3.79%) unigenes were mapped into 118 pathways by searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). Differentially expressed genes (DEG) analysis identified 3, 16 and 5,899 DEGs from the comparison of 7Y vs. 15Y, 7Y vs. 21Y and 15Y vs. 21Y, respectively, in the immature xylem tissues, including 2,638 significantly up-regulated and 3,280 significantly down-regulated genes. Besides, five NAC transcription factors, 190 MYB transcription factors, and 34 WRKY transcription factors were identified respectively from Chinese fir transcriptome. Conclusion: Our results revealed the active transcriptional pathways and identified the DEGs at different cultivation phases of Chinese fir wood formation. This transcriptome dataset will aid in understanding and carrying out future studies on the molecular basis of Chinese fir wood formation and contribute to future artificial production and applications.

scholarly journals Key role of the motor protein Kinesin 13B in the activity of homeodomain-leucine zipper I transcription factors

2020 ◽  
Vol 71 (20) ◽  
pp. 6282-6296
Author(s):  
Virginia Natali Miguel ◽  
Karina Fabiana Ribichich ◽  
Jorge Ignacio Giacomelli ◽  
Raquel Lia Chan
Keyword(s):  
Transcription Factors ◽  
Leucine Zipper ◽  
Molecular Mechanisms ◽  
Vascular Tissue ◽  
Expression Patterns ◽  
Motor Protein ◽  
Bimolecular Fluorescence Complementation ◽  
Yeast Two Hybrid ◽  
Cauline Leaf ◽  
Two Hybrid

Abstract The sunflower (Helianthus annuus) homeodomain-leucine zipper I transcription factor HaHB11 conferred differential phenotypic features when it was expressed in Arabidopsis, alfalfa, and maize plants. Such differences were increased biomass, seed yield, and tolerance to flooding. To elucidate the molecular mechanisms leading to such traits and identify HaHB11-interacting proteins, a yeast two-hybrid screening of an Arabidopsis cDNA library was carried out using HaHB11 as bait. The sole protein identified with high confidence as interacting with HaHB11 was Kinesin 13B. The interaction was confirmed by bimolecular fluorescence complementation and by yeast two-hybrid assay. Kinesin 13B also interacted with AtHB7, the Arabidopsis closest ortholog of HaHB11. Histochemical analyses revealed an overlap between the expression patterns of the three genes in hypocotyls, apical meristems, young leaves, vascular tissue, axillary buds, cauline leaves, and cauline leaf nodes at different developmental stages. AtKinesin 13B mutants did not exhibit a differential phenotype when compared with controls; however, both HaHB11 and AtHB7 overexpressor plants lost, partially or totally, their differential phenotypic characteristics when crossed with such mutants. Altogether, the results indicated that Kinesin 13B is essential for the homeodomain-leucine zipper transcription factors I to exert their functions, probably via regulation of the intracellular distribution of these transcription factors by the motor protein.

scholarly journals Involvement of Transcription Factor Encoded by the Mouse mi Locus (MITF ) in Expression of p75 Receptor of Nerve Growth Factor in Cultured Mast Cells of Mice

Blood ◽  
1997 ◽  
Vol 90 (7) ◽  
pp. 2601-2608 ◽  
Author(s):  
Tomoko Jippo ◽  
Eiichi Morii ◽  
Kumiko Tsujino ◽  
Tohru Tsujimura ◽  
Young-Mi Lee ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Nerve Growth Factor ◽  
Growth Factor ◽  
Mast Cells ◽  
Leucine Zipper ◽  
Poor Response ◽  
Nerve Growth ◽  
Helix Loop Helix ◽  
3T3 Fibroblasts ◽  
Direct Binding

The mi locus of mice encodes a member of the basic-helix-loop-helix-leucine zipper (bHLH-Zip) protein family of transcription factors (hereafter called MITF ). Cultured mast cells (CMCs) of mi/mi genotype showed a poor response to nerve growth factor (NGF ). Addition of NGF to the suboptimal dose of interleukin-3 (IL-3) increased the plating efficiency of normal (+/+) CMCs but not mi/mi CMCs. Although +/+ CMCs were berberine sulfate–negative when cultured with IL-3, +/+ CMCs became berberine sulfate–positive when cultured in the presence of both IL-3 and NGF, which suggested increased heparin content. In contrast, NGF did not influence the phenotype of mi/mi CMCs. The poor response of mi/mi CMCs to NGF was attributed to the deficient expression of p75 NGF receptor. The purpose of the present study is to examine the effect of MITF on p75 gene transcription. Overexpression of +-MITF or mi-MITF was observed in mi/mi CMCs to which cDNA encoding each type of MITF had been introduced using the retroviral vector. Overexpression of +-MITF but not of mi-MITF normalized the expression of p75 and the above-mentioned poor responses of mi/mi CMCs to NGF, indicating the involvement of +-MITF in p75 gene transactivation. Then, we analyzed the promoter of the p75 gene. Two CANNTG motifs recognized by bHLH-Zip–type transcription factors were conserved between the mouse and rat p75 promoters. One of these two CANNTG motifs was specifically bound by +-MITF. When the luciferase gene under the control of the p75 promoter was cotransfected into NIH/3T3 fibroblasts with cDNA encoding +-MITF or mi-MITF, luciferase activity increased significantly only when +-MITF cDNA was cotransfected. The mutation of this CANNTG motif abolished the transactivation effect of +-MITF, indicating that +-MITF transactivated the p75 gene, at least in part, through direct binding.

scholarly journals Genetic Interactions Between Aspergillus fumigatus Basic Leucine Zipper (bZIP) Transcription Factors AtfA, AtfB, AtfC, and AtfD

2021 ◽  
Vol 2 ◽  
Author(s):  
Lilian Pereira Silva ◽  
Maria Augusta Crivelente Horta ◽  
Gustavo Henrique Goldman
Keyword(s):  
Transcription Factors ◽  
Aspergillus Fumigatus ◽  
Leucine Zipper ◽  
Galleria Mellonella ◽  
Carbon Sources ◽  
Normal Growth ◽  
Genetic Interactions ◽  
Basic Leucine Zipper ◽  
Physical Interactions ◽  
Null Mutants

Aspergillus fumigatus is an opportunistic fungus, capable of causing Invasive Aspergillosis in immunocompromised patients, recently transplanted or undergoing chemotherapy. In the present work, we continued the investigation on A. fumigatus AtfA-D transcription factors (TFs) characterizing possible genetic and physical interactions between them after normal growth and stressing conditions. We constructed double null mutants for all the possible combinations of ΔatfA-, -B, -C, and -D, and look into their susceptibility to different stressing conditions. Our results indicate complex genetic interactions among these TFs that could impact the response to different kinds of stressful conditions. AtfA-D interactions also affect the A. fumigatus virulence in Galleria mellonella. AtfA:GFP is ~97% located in the nucleus while about 20–30% of AtfB, -C, and -D:GFP locate into the nucleus in the absence of any stress. Under stressing conditions, AtfB, -C, and -D:GFP translocate to the nucleus about 60–80% upon the addition of sorbitol or H2O2. These four TFs are also interacting physically forming all the possible combinations of heterodimers. We also identified that AtfA-D physically interact with the MAPK SakA in the absence of any stress and upon osmotic and cell wall stresses. They are involved in the accumulation of trehalose, glycogen and metabolic assimilation of different carbon sources.

scholarly journals Involvement of Transcription Factor Encoded by the Mouse mi Locus (MITF ) in Expression of p75 Receptor of Nerve Growth Factor in Cultured Mast Cells of Mice

Blood ◽  
1997 ◽  
Vol 90 (7) ◽  
pp. 2601-2608 ◽  
Author(s):  
Tomoko Jippo ◽  
Eiichi Morii ◽  
Kumiko Tsujino ◽  
Tohru Tsujimura ◽  
Young-Mi Lee ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Nerve Growth Factor ◽  
Growth Factor ◽  
Mast Cells ◽  
Leucine Zipper ◽  
Poor Response ◽  
Nerve Growth ◽  
Helix Loop Helix ◽  
3T3 Fibroblasts ◽  
Direct Binding

Abstract The mi locus of mice encodes a member of the basic-helix-loop-helix-leucine zipper (bHLH-Zip) protein family of transcription factors (hereafter called MITF ). Cultured mast cells (CMCs) of mi/mi genotype showed a poor response to nerve growth factor (NGF ). Addition of NGF to the suboptimal dose of interleukin-3 (IL-3) increased the plating efficiency of normal (+/+) CMCs but not mi/mi CMCs. Although +/+ CMCs were berberine sulfate–negative when cultured with IL-3, +/+ CMCs became berberine sulfate–positive when cultured in the presence of both IL-3 and NGF, which suggested increased heparin content. In contrast, NGF did not influence the phenotype of mi/mi CMCs. The poor response of mi/mi CMCs to NGF was attributed to the deficient expression of p75 NGF receptor. The purpose of the present study is to examine the effect of MITF on p75 gene transcription. Overexpression of +-MITF or mi-MITF was observed in mi/mi CMCs to which cDNA encoding each type of MITF had been introduced using the retroviral vector. Overexpression of +-MITF but not of mi-MITF normalized the expression of p75 and the above-mentioned poor responses of mi/mi CMCs to NGF, indicating the involvement of +-MITF in p75 gene transactivation. Then, we analyzed the promoter of the p75 gene. Two CANNTG motifs recognized by bHLH-Zip–type transcription factors were conserved between the mouse and rat p75 promoters. One of these two CANNTG motifs was specifically bound by +-MITF. When the luciferase gene under the control of the p75 promoter was cotransfected into NIH/3T3 fibroblasts with cDNA encoding +-MITF or mi-MITF, luciferase activity increased significantly only when +-MITF cDNA was cotransfected. The mutation of this CANNTG motif abolished the transactivation effect of +-MITF, indicating that +-MITF transactivated the p75 gene, at least in part, through direct binding.

scholarly journals Mechanism of conditional partner selectivity in MITF/TFE family transcription factors with a conserved coiled coil stammer motif

2019 ◽  
Vol 48 (2) ◽  
pp. 934-948 ◽  
Author(s):  
Vivian Pogenberg ◽  
Josué Ballesteros-Álvarez ◽  
Romana Schober ◽  
Ingibjörg Sigvaldadóttir ◽  
Agnieszka Obarska-Kosinska ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
High Resolution ◽  
Nuclear Localization ◽  
Leucine Zipper ◽  
Coiled Coil ◽  
Fundamental Difference ◽  
Wild Type ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix

Abstract Interrupted dimeric coiled coil segments are found in a broad range of proteins and generally confer selective functional properties such as binding to specific ligands. However, there is only one documented case of a basic-helix–loop–helix leucine zipper transcription factor—microphthalmia-associated transcription factor (MITF)—in which an insertion of a three-residue stammer serves as a determinant of conditional partner selectivity. To unravel the molecular principles of this selectivity, we have analyzed the high-resolution structures of stammer-containing MITF and an engineered stammer-less MITF variant, which comprises an uninterrupted symmetric coiled coil. Despite this fundamental difference, both MITF structures reveal identical flanking in-phase coiled coil arrangements, gained by helical over-winding and local asymmetry in wild-type MITF across the stammer region. These conserved structural properties allow the maintenance of a proper functional readout in terms of nuclear localization and binding to specific DNA-response motifs regardless of the presence of the stammer. By contrast, MITF heterodimer formation with other bHLH-Zip transcription factors is only permissive when both factors contain either the same type of inserted stammer or no insert. Our data illustrate a unique principle of conditional partner selectivity within the wide arsenal of transcription factors with specific partner-dependent functional readouts.

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