Comparative Transcriptome Profiling Reveals Defense-Related Genes against Meloidogyne incognita Invasion in Tobacco

Root-knot nematodes Meloidogyne incognita are one of the most destructive pathogens, causing severe losses to tobacco productivity and quality. However, the underlying resistance mechanism of tobacco to M. incognita is not clear. In this study, two tobacco genotypes, K326 and Changbohuang, which are resistant and susceptible to M. incognita, respectively, were used for RNA-sequencing analysis. An average of 35 million clean reads were obtained. Compared with their expression levels in non-infected plants of the same genotype, 4354 and 545 differentially expressed genes (DEGs) were detected in the resistant and susceptible genotype, respectively, after M. incognita invasion. Overall, 291 DEGs, involved in diverse biological processes, were common between the two genotypes. Genes encoding toxic compound synthesis, cell wall modification, reactive oxygen species and the oxidative burst, salicylic acid signal transduction, and production of some other metabolites were putatively associated with tobacco resistance to M. incognita. In particular, the complex resistance response needed to overcome M. incognita invasion may be regulated by several transcription factors, such as the ethylene response factor, MYB, basic helix–loop–helix transcription factor, and indole acetic acid–leucine-resistant transcription factor. These results may aid in the identification of potential genes of resistance to M. incognita for tobacco cultivar improvement.

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NeuroM, a neural helix-loop-helix transcription factor, defines a new transition stage in neurogenesis

Development ◽

10.1242/dev.124.17.3263 ◽

1997 ◽

Vol 124 (17) ◽

pp. 3263-3272 ◽

Cited By ~ 11

Author(s):

T. Roztocil ◽

L. Matter-Sadzinski ◽

C. Alliod ◽

M. Ballivet ◽

J.M. Matter

Keyword(s):

Nervous System ◽

Transcription Factor ◽

Mitotic Cycle ◽

Ventricular Zone ◽

Helix Loop Helix ◽

E Box ◽

Genes Encoding ◽

Developing Nervous System

Genes encoding transcription factors of the helix-loop-helix family are essential for the development of the nervous system in Drosophila and vertebrates. Screens of an embryonic chick neural cDNA library have yielded NeuroM, a novel neural-specific helix-loop-helix transcription factor related to the Drosophila proneural gene atonal. The NeuroM protein most closely resembles the vertebrate NeuroD and Nex1/MATH2 factors, and is capable of transactivating an E-box promoter in vivo. In situ hybridization studies have been conducted, in conjunction with pulse-labeling of S-phase nuclei, to compare NeuroM to NeuroD expression in the developing nervous system. In spinal cord and optic tectum, NeuroM expression precedes that of NeuroD. It is transient and restricted to cells lining the ventricular zone that have ceased proliferating but have not yet begun to migrate into the outer layers. In retina, NeuroM is also transiently expressed in cells as they withdraw from the mitotic cycle, but persists in horizontal and bipolar neurons until full differentiation, assuming an expression pattern exactly complementary to NeuroD. In the peripheral nervous system, NeuroM expression closely follows cell proliferation, suggesting that it intervenes at a similar developmental juncture in all parts of the nervous system. We propose that availability of the NeuroM helix-loop-helix factor defines a new stage in neurogenesis, at the transition between undifferentiated, premigratory and differentiating, migratory neural precursors.

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The bHLH transcription factor BIS1 controls the iridoid branch of the monoterpenoid indole alkaloid pathway in Catharanthus roseus

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1504951112 ◽

2015 ◽

Vol 112 (26) ◽

pp. 8130-8135 ◽

Cited By ~ 88

Author(s):

Alex Van Moerkercke ◽

Priscille Steensma ◽

Fabian Schweizer ◽

Jacob Pollier ◽

Ivo Gariboldi ◽

...

Keyword(s):

Transcription Factor ◽

Catharanthus Roseus ◽

Transcriptional Activation ◽

Indole Alkaloid ◽

Bioactive Metabolites ◽

Bhlh Transcription Factor ◽

Ethylene Response Factor ◽

Madagascar Periwinkle ◽

Genes Encoding ◽

Monoterpenoid Indole Alkaloid

Plants make specialized bioactive metabolites to defend themselves against attackers. The conserved control mechanisms are based on transcriptional activation of the respective plant species-specific biosynthetic pathways by the phytohormone jasmonate. Knowledge of the transcription factors involved, particularly in terpenoid biosynthesis, remains fragmentary. By transcriptome analysis and functional screens in the medicinal plant Catharanthus roseus (Madagascar periwinkle), the unique source of the monoterpenoid indole alkaloid (MIA)-type anticancer drugs vincristine and vinblastine, we identified a jasmonate-regulated basic helix–loop–helix (bHLH) transcription factor from clade IVa inducing the monoterpenoid branch of the MIA pathway. The bHLH iridoid synthesis 1 (BIS1) transcription factor transactivated the expression of all of the genes encoding the enzymes that catalyze the sequential conversion of the ubiquitous terpenoid precursor geranyl diphosphate to the iridoid loganic acid. BIS1 acted in a complementary manner to the previously characterized ethylene response factor Octadecanoid derivative-Responsive Catharanthus APETALA2-domain 3 (ORCA3) that transactivates the expression of several genes encoding the enzymes catalyzing the conversion of loganic acid to the downstream MIAs. In contrast to ORCA3, overexpression of BIS1 was sufficient to boost production of high-value iridoids and MIAs in C. roseus suspension cell cultures. Hence, BIS1 might be a metabolic engineering tool to produce sustainably high-value MIAs in C. roseus plants or cultures.

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Inhibitory Effect of the Transcription Factor Encoded by themi Mutant Allele in Cultured Mast Cells of Mice

Blood ◽

10.1182/blood.v93.4.1189.404k32_1189_1196 ◽

1999 ◽

Vol 93 (4) ◽

pp. 1189-1196 ◽

Cited By ~ 2

Author(s):

Akihiko Ito ◽

Eiichi Morii ◽

Dae-Ki Kim ◽

Tatsuki R. Kataoka ◽

Tomoko Jippo ◽

...

Keyword(s):

Transcription Factor ◽

Mast Cells ◽

Leucine Zipper ◽

Tryptophan Hydroxylase ◽

Cdna Probe ◽

Inhibitory Effect ◽

Northern Analysis ◽

Helix Loop Helix ◽

Genes Encoding ◽

Mouse Mast Cell

The mi locus of mice encodes a transcription factor of the basic-helix-loop-helix-leucine zipper protein family (MITF). The MITF encoded by the mutant mi allele (mi-MITF) deletes 1 of 4 consecutive arginines in the basic domain. The mice of mi/migenotype express mi-MITF, whereas the mice of tg/tggenotype have a transgene at the 5′ flanking region of themi gene and do not express any MITF. To investigate the function of mi-MITF in cultured mast cells (CMCs), we took two approaches. First, mRNA obtained from mi/mi CMCs ortg/tg CMCs was subtracted from complementary (c) DNA library of normal (+/+) CMCs, and the (+/+-mi/mi) and (+/+-tg/tg) subtraction libraries were obtained. When the number of clones that hybridized more efficiently with +/+ CMC cDNA probe than with mi/mi or tg/tg CMC cDNA probe was compared using Southern analysis, the number was larger in the (+/+-mi/mi) library than in the (+/+-tg/tg) library. Second, we compared mRNA expression of six genes betweenmi/mi and tg/tg CMCs by Northern analysis. The transcription of three genes encoding mouse mast cell proteases was impaired in both mi/mi and tg/tg CMCs. On the other hand, the transcription of three genes encoding c-kit receptor, tryptophan hydroxylase, and granzyme B was markedly reduced inmi/mi CMCs, but the reduction was significantly smaller intg/tg CMCs. These results indicated the inhibitory effect ofmi-MITF on the transactivation of particular genes in CMCs.

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Identification and function of phosphorylation in the glucose-regulated transcription factor ChREBP

Biochemical Journal ◽

10.1042/bj20071156 ◽

2008 ◽

Vol 411 (2) ◽

pp. 261-270 ◽

Cited By ~ 28

Author(s):

Nikolas G. Tsatsos ◽

Michael N. Davies ◽

Brennon L. O'callaghan ◽

Howard C. Towle

Keyword(s):

Transcription Factor ◽

High Glucose ◽

Leucine Zipper ◽

De Novo ◽

Regulatory Region ◽

De Novo Lipogenesis ◽

Nuclear Accumulation ◽

Helix Loop Helix ◽

Genes Encoding ◽

And Function

In the liver, induction of genes encoding enzymes involved in de novo lipogenesis occurs in response to increased glucose metabolism. ChREBP (carbohydrate-response-element-binding protein) is a basic helix–loop–helix/leucine zipper transcription factor that regulates expression of these genes. To evaluate the potential role of ChREBP phosphorylation in its regulation, we used MS to identify modified residues. In the present paper, we report the detection of multiple phosphorylation sites of ChREBP expressed in hepatocytes, several of which are only observed under high-glucose conditions. Mutation of each of these serine/threonine residues of ChREBP did not alter its ability to respond to glucose. However, mutation of five N-terminal phosphoacceptor sites resulted in a major decrease in activity under high-glucose conditions. These phosphorylated residues are located within a region of ChREBP (amino acids 1–197) that is critical for glucose regulation. Mutation of Ser56 within this region to an aspartate residue resulted in increased nuclear accumulation and activity under high-glucose conditions. Together, these data suggest that ChREBP activity is regulated by complex multisite phosphorylation patterns involving its N-terminal regulatory region.

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The Basic Helix-Loop-Helix Transcription Factor NeuroD1 Facilitates Interaction of Sp1 with the Secretin Gene Enhancer

Molecular and Cellular Biology ◽

10.1128/mcb.00438-07 ◽

2007 ◽

Vol 27 (22) ◽

pp. 7839-7847 ◽

Cited By ~ 18

Author(s):

Subir K. Ray ◽

Andrew B. Leiter

Keyword(s):

Transcription Factor ◽

Dna Binding ◽

Target Genes ◽

Zinc Fingers ◽

Homeodomain Proteins ◽

Basic Helix Loop Helix ◽

Helix Loop Helix ◽

Gene Enhancer ◽

Genes Encoding

ABSTRACT The basic helix-loop-helix transcription factor NeuroD1 is required for late events in neuronal differentiation, for maturation of pancreatic β cells, and for terminal differentiation of enteroendocrine cells expressing the hormone secretin. NeuroD1-null mice demonstrated that this protein is essential for expression of the secretin gene in the murine intestine, and yet it is a relatively weak transcriptional activator by itself. The present study shows that Sp1 and NeuroD1 synergistically activate transcription of the secretin gene. NeuroD1, but not its widely expressed dimerization partner E12, physically interacts with the C-terminal 167 amino acids of Sp1, which include its DNA binding zinc fingers. NeuroD1 stabilizes Sp1 DNA binding to an adjacent Sp1 binding site on the promoter to generate a higher-order DNA-protein complex containing both proteins and facilitates Sp1 occupancy of the secretin promoter in vivo. NeuroD-dependent transcription of the genes encoding the hormones insulin and proopiomelanocortin is potentiated by lineage-specific homeodomain proteins. The stabilization of binding of the widely expressed transcription factor Sp1 to the secretin promoter by NeuroD represents a distinct mechanism from other NeuroD target genes for increasing NeuroD-dependent transcription.

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Genetic and physiological characterization of sunflower resistance provided by the wild-derived OrDeb2 gene against highly virulent races of Orobanche cumana Wallr

Theoretical and Applied Genetics ◽

10.1007/s00122-021-03979-9 ◽

2021 ◽

Author(s):

Mónica Fernández-Aparicio ◽

Lidia del Moral ◽

Stéphane Muños ◽

Leonardo Velasco ◽

Begoña Pérez-Vich

Keyword(s):

Genetic Resistance ◽

Resistance Mechanism ◽

Kinase Domain ◽

Genomic Region ◽

Snp Markers ◽

Resistance Response ◽

Physiological Characterization ◽

Orobanche Cumana ◽

Genes Encoding ◽

Highly Virulent

Abstract Key message OrDeb2 confers post-attachment resistance to Orobanche cumana and is located in a 1.38 Mbp genomic interval containing a cluster of receptor-like kinase and receptor-like protein genes with nine high-confidence candidates. Abstract Sunflower broomrape is a holoparasitic angiosperm that parasitizes on sunflower roots, severely constraining crop yield. Breeding for resistance is the most effective method of control. OrDeb2 is a dominant resistance gene introgressed into cultivated sunflower from a wild-related species that confers resistance to highly virulent broomrape races. The objectives of this study were as follows: (i) locate OrDeb2 into the sunflower genome and determine putative candidate genes and (ii) characterize its underlying resistance mechanism. A segregating population from a cross between the sunflower resistant line DEB2, carrying OrDeb2, and a susceptible line was phenotyped for broomrape resistance in four experiments, including different environments and two broomrape races (FGV and GTK). This population was also densely genotyped with microsatellite and SNP markers, which allowed locating OrDeb2 within a 0.9 cM interval in the upper half of Chromosome 4. This interval corresponded to a 1.38 Mbp genomic region of the sunflower reference genome that contained a cluster of genes encoding LRR (leucine-rich repeat) receptor-like proteins lacking a cytoplasmic kinase domain and receptor-like kinases with one or two kinase domains and lacking an extracellular LRR region, which were valuable candidates for OrDeb2. Rhizotron and histological studies showed that OrDeb2 determines a post-attachment resistance response that blocks O. cumana development mainly at the cortex before the establishment of host-parasite vascular connections. This study will contribute to understand the interaction between crops and parasitic weeds, to establish durable breeding strategies based on genetic resistance and provide useful tools for marker-assisted selection and OrDeb2 map-based cloning.

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Copper economy in Chlamydomonas: Prioritized allocation and reallocation of copper to respiration vs. photosynthesis

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1422492112 ◽

2015 ◽

Vol 112 (9) ◽

pp. 2644-2651 ◽

Cited By ~ 32

Author(s):

Janette Kropat ◽

Sean D. Gallaher ◽

Eugen I. Urzica ◽

Stacie S. Nakamoto ◽

Daniela Strenkert ◽

...

Keyword(s):

Transcription Factor ◽

Primary Productivity ◽

Copper Deficiency ◽

Response Regulator ◽

Transcriptome Profiling ◽

Inorganic Elements ◽

Gene Encoding ◽

Copper Protein ◽

Genes Encoding ◽

Copper Availability

Inorganic elements, although required only in trace amounts, permit life and primary productivity because of their functions in catalysis. Every organism has a minimal requirement of each metal based on the intracellular abundance of proteins that use inorganic cofactors, but elemental sparing mechanisms can reduce this quota. A well-studied copper-sparing mechanism that operates in microalgae faced with copper deficiency is the replacement of the abundant copper protein plastocyanin with a heme-containing substitute, cytochrome (Cyt) c6. This switch, which is dependent on a copper-sensing transcription factor, copper response regulator 1 (CRR1), dramatically reduces the copper quota. We show here that in a situation of marginal copper availability, copper is preferentially allocated from plastocyanin, whose function is dispensable, to other more critical copper-dependent enzymes like Cyt oxidase and a ferroxidase. In the absence of an extracellular source, copper allocation to Cyt oxidase includes CRR1-dependent proteolysis of plastocyanin and quantitative recycling of the copper cofactor from plastocyanin to Cyt oxidase. Transcriptome profiling identifies a gene encoding a Zn-metalloprotease, as a candidate effecting copper recycling. One reason for the retention of genes encoding both plastocyanin and Cyt c6 in algal and cyanobacterial genomes might be because plastocyanin provides a competitive advantage in copper-depleted environments as a ready source of copper.

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Transcriptome profiling reveals signaling conditions dictating human spermatogonia fate in vitro

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2000362117 ◽

2020 ◽

Vol 117 (30) ◽

pp. 17832-17841 ◽

Cited By ~ 3

Author(s):

Kun Tan ◽

Hye-Won Song ◽

Merlin Thompson ◽

Sarah Munyoki ◽

Meena Sukhwani ◽

...

Keyword(s):

Signaling Pathways ◽

Rna Sequencing ◽

Surface Protein ◽

Transcriptome Profiling ◽

Sequencing Analysis ◽

Akt Inhibitor ◽

Genes Encoding ◽

Full Complement ◽

Pathway Inhibition

Spermatogonial stem cells (SSCs) are essential for the generation of sperm and have potential therapeutic value for treating male infertility, which afflicts >100 million men world-wide. While much has been learned about rodent SSCs, human SSCs remain poorly understood. Here, we molecularly characterize human SSCs and define conditions favoring their culture. To achieve this, we first identified a cell-surface protein, PLPPR3, that allowed purification of human primitive undifferentiated spermatogonia (uSPG) highly enriched for SSCs. Comparative RNA-sequencing analysis of these enriched SSCs with differentiating SPG (KIT+cells) revealed the full complement of genes that shift expression during this developmental transition, including genes encoding key components in the TGF-β, GDNF, AKT, and JAK-STAT signaling pathways. We examined the effect of manipulating these signaling pathways on cultured human SPG using both conventional approaches and single-cell RNA-sequencing analysis. This revealed that GDNF and BMP8B broadly support human SPG culture, while activin A selectively supports more advanced human SPG. One condition—AKT pathway inhibition—had the unique ability to selectively support the culture of primitive human uSPG. This raises the possibility that supplementation with an AKT inhibitor could be used to culture human SSCs in vitro for therapeutic applications.

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Transcriptome Profiling Reveals Inhibitory Effect of Down-regulated ZBTB38 gene on the Transcriptional Regulation of Tumor Cells Proliferation

10.1101/350223 ◽

2018 ◽

Author(s):

Jie Chen ◽

Chaofeng Xing ◽

Haosen Wang ◽

Zengmeng Zhang ◽

Daolun Yu ◽

...

Keyword(s):

Transcription Factor ◽

Tumor Cells ◽

Differentially Expressed Genes ◽

Zinc Finger Protein ◽

Enrichment Analysis ◽

Transcriptome Profiling ◽

Inhibitory Effect ◽

Differentially Expressed ◽

Pathway Enrichment Analysis ◽

Sequencing Analysis

AbstractTranscription factor ZBTB38 belongs to the zinc finger protein family and contains the typical BTB domains. Only several predicted BTB domain-containing proteins encoded in the human genome have been functionally characterized. No relevant studies have been reported concerning the effect of down-regulated ZBTB38 gene expression on tumor cells through transcriptome analysis. In the present study, 2,438 differentially expressed genes in ZBTB38−/− SH-SY5Y cells were obtained via high-throughput transcriptome sequencing analysis, 83.5% of which was down-regulated. Furthermore, GO functional clustering and KEGG pathway enrichment analysis of these differentially expressed genes (DEGs) revealed that the knocked-down transcription factor ZBTB38 interacted with p53 and arrested cell cycles to inhibit the proliferation of the tumor cells. Besides, it also significantly down-regulated the expressions of PTEN, a “molecular switch” of the PI3K/Akt signaling pathway, and RB1CC1, the key gene for autophagy initiation, and blocked autophagy to accelerate the apoptosis of tumor cells. ZBTB38−/− SH-SY5Y cells were investigated at the whole transcriptome level and key DEGs were screened in the present study for the first time, providing a theoretical foundation for exploring the molecular mechanism of inhibition of tumor cell proliferation and targeted anti-tumor therapies.

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Inhibitory Effect of the Transcription Factor Encoded by themi Mutant Allele in Cultured Mast Cells of Mice

Blood ◽

10.1182/blood.v93.4.1189 ◽

1999 ◽

Vol 93 (4) ◽

pp. 1189-1196 ◽

Cited By ~ 38

Author(s):

Akihiko Ito ◽

Eiichi Morii ◽

Dae-Ki Kim ◽

Tatsuki R. Kataoka ◽

Tomoko Jippo ◽

...

Keyword(s):

Transcription Factor ◽

Mast Cells ◽

Leucine Zipper ◽

Tryptophan Hydroxylase ◽

Cdna Probe ◽

Inhibitory Effect ◽

Northern Analysis ◽

Helix Loop Helix ◽

Genes Encoding ◽

Mouse Mast Cell

Abstract The mi locus of mice encodes a transcription factor of the basic-helix-loop-helix-leucine zipper protein family (MITF). The MITF encoded by the mutant mi allele (mi-MITF) deletes 1 of 4 consecutive arginines in the basic domain. The mice of mi/migenotype express mi-MITF, whereas the mice of tg/tggenotype have a transgene at the 5′ flanking region of themi gene and do not express any MITF. To investigate the function of mi-MITF in cultured mast cells (CMCs), we took two approaches. First, mRNA obtained from mi/mi CMCs ortg/tg CMCs was subtracted from complementary (c) DNA library of normal (+/+) CMCs, and the (+/+-mi/mi) and (+/+-tg/tg) subtraction libraries were obtained. When the number of clones that hybridized more efficiently with +/+ CMC cDNA probe than with mi/mi or tg/tg CMC cDNA probe was compared using Southern analysis, the number was larger in the (+/+-mi/mi) library than in the (+/+-tg/tg) library. Second, we compared mRNA expression of six genes betweenmi/mi and tg/tg CMCs by Northern analysis. The transcription of three genes encoding mouse mast cell proteases was impaired in both mi/mi and tg/tg CMCs. On the other hand, the transcription of three genes encoding c-kit receptor, tryptophan hydroxylase, and granzyme B was markedly reduced inmi/mi CMCs, but the reduction was significantly smaller intg/tg CMCs. These results indicated the inhibitory effect ofmi-MITF on the transactivation of particular genes in CMCs.

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