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Identification and characterization of a putative basic helix-loop-helix (bHLH) transcription factor interacting with calcineurin in C. elegans

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MOLECULES AND CELLS 2009年第5期28卷 455-461页

作者： Lee, Soo-Ung Song, Hyun-Ok Lee, Wonhae Singaravelu, Gunasekaran Yu, Jae-Ran Park, Woo-Yoon Konkuk Univ Sch Med Dept Environm & Trop Med Seoul 143701 South Korea Gwangju Inst Sci & Technol Dept Life Sci Kwangju 500712 South Korea Rutgers State Univ Waksman Inst Piscataway NJ 08854 USA Chungbuk Natl Univ Coll Med Dept Radiat Oncol Cheongju 361763 South Korea

Calcineurin is a Ca2+/Calmodulin activated Ser/Thr phosphatase that is well conserved from yeast to human. It is composed of catalytic subunit A (CnA) and regulatory subunit B (CnB). C. elegans homolog of CnA and CnB has been annotated to tax-6 and cnb-1, respectively and in vivo function of both genes has been intensively studied. In C. elegans, calcineurin play roles in various signaling pathways such as fertility, movement, body size regulation and serotonin-mediated egg laying. In order to understand additional signaling pathway(s) in which calcineurin functions, we screened for binding proteins of TAX-6 and found a novel binding protein, HLH-11. The HLH-11, a member of basic helix-loop-helix (bHLH) proteins, is a putative counterpart of human AP4 transcription factor. Previously bHLH transcription factors have been implicated to regulate many developmental processes such as cell proliferation and differentiation, sex determination and myogenesis. However, the in vivo function of hlh-11 is largely unknown. Here, we show that hlh-11 is expressed in pharynx, intestine, nerve cords, anal depressor and vuvla muscles where calcineurin is also expressed. Mutant analyses reveal that hlh-11 may have role(s) in regulating body size and reproduction. More interestingly, genetic epistasis suggests that hlh-11 may function to regulate serotonin-mediated egg laying at the downstream of tax-6.

关键词： basic helix-loop-helix calcineurin C. elegans egg laying HLH-11

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Phylogenetic Analysis of Zebrafish basic helix-loop-helix Transcription Factors

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JOURNAL OF MOLECULAR EVOLUTION 2009年第6期68卷 629-640页

作者： Wang, Yong Chen, Keping Yao, Qin Zheng, Xiaodong Yang, Zhe Jiangsu Univ Inst Life Sci Zhenjiang 212013 Peoples R China Jiangsu Univ Dept Biotechnol Sch Food & Biol Engn Zhenjiang 212013 Peoples R China

The basic helix-loop-helix (bHLH) proteins play important regulatory roles in eukaryotic developmental processes including neurogenesis, myogenesis, hematopoiesis, sex determination, and gut development. Zebrafish is a good model organism for developmental biology. In this study, we identified 139 bHLH genes encoded in the zebrafish genome. Phylogenetic analyses revealed that zebrafish has 58, 29, 21, 5, 19, and 5 bHLH members in groups A, B, C, D, E, and F, respectively, while 2 members were classified as "orphan." A comparison between zebrafish and human bHLH repertoires suggested that both organisms have a certain number of specific bHLH members. Eight zebrafish bHLH genes were found to have multiple coding regions in the genome. Two of these, Bmal1 and MITF, are good anchor genes for identification of fish-specific whole-genome duplication events in comparison with mouse and chicken genomes. The present study provides useful information for future studies on gene family evolution and vertebrate development.

关键词： basic helix-loop-helix Phylogenesis Transcription factor Zebrafish

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OsMPK3 is a TEY-type rice MAPK in Group C and phosphorylates OsbHLH65, a transcription factor binding to the E-box element

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PLANT CELL REPORTS 2014年第8期33卷 1343-1353页

作者： Shin, Hyun-Young You, Min Kyoung Jeung, Ji Ung Shin, Jeong Sheop Korea Univ Div Life Sci Seoul 136701 South Korea Kyung Hee Univ Coll Life Sci Gyeonggi Do 446701 South Korea Rural Dev Adm Natl Inst Crop Sci Suwon 441100 South Korea

OsMPK3 is a TEY-type rice MAPK belonging to Group C and directly phosphorylates OsbHLH65 in the nucleus. OsMPK3 and OsbHLH65 are induced by biotic stress and defense-related hormones. Mitogen-activated protein kinases (MAPKs) are involved in the majority of signaling pathways that regulate plant development and stress tolerance via the phosphorylation of target molecules. Plant MAPKs are classified into two subtypes, TEY and TDY, according to the TxY (x = E or D) motif in their activation loop, and the TDY motif is unique to plant MAPKs. In rice, 17 MAPKs have been classified into six groups. To date, the functions of many TDY-type rice MAPKs have been characterized, but little is known of the TEY-type MAPKs in Group C and their possible target substrates. In the study reported here, we determined that a TEY-type rice MAPK belonging to subgroup C, named OsMPK3, phosphorylates its substrate OsbHLH65 in the nucleus. Our electrophoresis mobility shift assay results revealed that OsbHLH65 specifically binds to the E-box cis-element, but not to the G-box. Both OsMPK3 and OsbHLH65 were induced by treatments with rice blast (Magnaporthe grisea), brown planthopper (Nilaparvata lugens), and defense-related hormones, such as methyl jasmonic acid and salicylic acid. Our results suggest the possibility that OsMPK3 contributes to the defense signal transduction by phosphorylating the basic helix-loop-helix transcription factor.

关键词： Oryza sativa Magnaporthe grisea MAP kinase basic helix-loop-helix Biotic stress E-box cis-element

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ATF3 is a novel nuclear marker for migrating ependymal stem cells in the rat spinal cord

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STEM CELL RESEARCH 2014年第3期12卷 815-827页

作者： Mladinic, Miranda Bianchetti, Elena Dekanic, Ana Mazzone, Graciela L. Nistri, Andrea SISSA Int Sch Adv Studies Dept Neurosci I-34014 Trieste Italy Ist Med Fis & Riabilitaz SPINAL Udine Italy Univ Rijeka Dept Biotechnol Rijeka 51000 Croatia

The present study identified ATF3 as a novel dynamic marker for ependymal stem/progenitor cells (nestin, vimentin and SOX2 positive) around the central canal of the neonatal or adult rat spinal cord. While quiescent ependymal cells showed cytoplasmic ATF3 expression, during 6-24 h in vitro these cells mobilized and acquired intense nuclear ATF3 staining. Their migratory pattern followed a centrifugal pathway toward the dorsal and ventral funiculi, reminiscent of the rostral migratory stream of the brain subventricular stem cells. Thus, the chain cell formation was, by analogy, termed funicular migratory stream (FMS). The FMS process preceded the strong proliferation of ependymal cells occurring only after 24 h in vitro. Pharmacological inhibition of MAPK-p38 and JNK/c-Jun (upstream effectors of ATF3 activation) prevented the FMS mobilization of ATF3 nuclear-positive cells. Excitotoxicity or ischemia-like conditions, reported to evoke neuronal and glial injury, did not further enhance migration of ependymal cells at 24 h, suggesting that, at this early stage of damage, the FMS phenomenon had peaked and that more extensive repair processes are delayed beyond this time point. ATF3 is, therefore, useful to identify activation and migration of endogenous stem cells of the rat spinal cord in vitro. (C) 2014 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://***/licenses/by-nc-nd/3.0/).

关键词： ATF3 activating transcription factor AU arbitrary units bHLH basic helix-loop-helix bZIP basic Leucine Zipper CC central canal CREB cAMP responsive element-binding CSF cerebrospinal fluid DAPI 4,6-diamidino-2-phenylindole DCX doublecourtin EdU 5-ethynyl-20-deoxyuridine FMS funicular migratory stream GFAP glial fibrillary acidic protein MAPK mitogen-activated protein kinases PM pathological medium RMS rostral migratory stream SPCs stem and progenitor cells TBP TATA binding protein

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Gene expression is dynamically regulated in retinal progenitor cells prior to and during overt cellular differentiation

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GENE EXPRESSION PATTERNS 2014年第1期14卷 42-54页

作者： Dixit, Rajiv Tachibana, Nobuhiko Touahri, Yacine Zinyk, Dawn Logan, Cairine Schuurmans, Carol Univ Calgary Dept Biochem & Mol Biol Calgary AB Canada Univ Calgary Dept Cell Biol & Anat Calgary AB Canada Univ Calgary Hotchkiss Brain Inst Calgary AB Canada Univ Calgary Alberta Childrens Hosp Res Inst Calgary AB Canada

The retina is comprised of one glial and six neuronal populations that are generated from a multipotent pool of retinal progenitor cells (RPCs) during development. To give rise to these different cell types, RPCs undergo temporal identity transitions, displaying distinct gene expression profiles at different stages of differentiation. Little, however, is known about temporal differences in RPC identities prior to the onset of overt cellular differentiation, during the period when a retinal identity is gradually acquired. Here we examined the sequential onset of expression of regional markers (i.e., homeodomain transcription factors) and cell fate determinants (i.e., basic-helix-loop-helix transcription factors and neurogenic genes) in RPCs from the earliest appearance of a morphologically-distinct retina. By performing a comparative analysis of the expression of a panel of 27 homeodomain, basic-helix-loop-helix and Notch pathway genes between embryonic day (E) 8.75 and postnatal day (P) 9, we identified six distinct RPC molecular profiles. At E8.75, the earliest stage assayed, murine RPCs expressed five homeodomain genes and a single neurogenic gene (Pax6, Six3, Six6, Rx, Otx2, Hes1). This early gene expression profile was remarkably similar to that of 'early' RPCs in the amphibian ciliary marginal zone (CMZ), where RPCs are compart-mentalised according to developmental stage, and homologs of Pax6, Six3 and Rx are expressed in the 'early' stem cell zone. As development proceeds, expression of additional homeodomain, bHLH and neurogenic genes was gradually initiated in murine RPCs, allowing distinct genetic profiles to also be defined at E9.5, E10.5, E12.5, E15.5 and PO. In addition, RPCs in the postnatal ciliary margin, where retinal stem cells are retained throughout life, displayed a unique molecular signature, expressing all of the early-onset genes as well as several late-onset markers, indicative of a 'mixed' temporal identity. Taken together, the identificatio

关键词： Retinal progenitor cells basic helix-loop-helix Homeodomain Transcription factors Neurogenic genes Temporal sequence Ciliary margin Mouse

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The bHLH proteins BEE and BIM positively modulate the shade avoidance syndrome in Arabidopsis seedlings

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PLANT JOURNAL 2013年第6期75卷 989-1002页

作者： Cifuentes-Esquivel, Nicolas Bou-Torrent, Jordi Galstyan, Anahit Gallemi, Marcal Sessa, Giovanna Salla Martret, Merce Roig-Villanova, Irma Ruberti, Ida Martinez-Garcia, Jaime F. Univ Barcelona UAB IRTA CSICCRAG Barcelona 08193 Spain CNR Inst Mol Biol & Pathol I-00185 Rome Italy Inst Catalana Recerca & Estudis Avancats Barcelona 08010 Spain

The shade avoidance syndrome (SAS) refers to a set of plant responses initiated after perception by the phytochromes of light with a reduced red to far-red ratio, indicative of vegetation proximity or shade. These responses, including elongation growth, anticipate eventual shading from potential competitor vegetation by overgrowing neighboring plants or flowering to ensure production of viable seeds for the next generation. In Arabidopsis thaliana seedlings, the SAS includes dramatic changes in gene expression, such as induction of PHYTOCHROME RAPIDLY REGULATED 1 (PAR1), encoding an atypical basic helix-loop-helix (bHLH) protein that acts as a transcriptional co-factor to repress hypocotyl elongation. Indeed, PAR1 has been proposed to act fundamentally as a dominant negative antagonist of conventional bHLH transcription factors by forming heterodimers with them to prevent their binding to DNA or other transcription factors. Here we report the identification of PAR1-interacting factors, including the brassinosteroid signaling components BR-ENHANCED EXPRESSION (BEE) and BES1-INTERACTING MYC-LIKE (BIM), and characterize their role as networked positive regulators of SAS hypocotyl responses. We provide genetic evidence that these bHLH transcriptional regulators not only control plant growth and development under shade and non-shade conditions, but are also redundant in the control of plant viability. Our results suggest that SAS responses are initiated as a consequence of a new balance of transcriptional regulators within the pre-existing bHLH network triggered by plant proximity, eventually causing hypocotyls to elongate.

关键词： shade avoidance syndrome hypocotyl elongation basic helix-loop-helix BEEs and BIMs PAR1 transcriptional co-factors Arabidopsis thaliana

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helix-loop-helix Protein Id2 Stabilizes Mammalian Circadian Oscillation Under Constant Light Conditions

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ZOOLOGICAL SCIENCE 2013年第12期30卷 1011-1018页

作者： Adachi, Akihito A. Fujioka, Atsuko Nagano, Mamoru Masumoto, Koh-hei Takumi, Toru Yoshimura, Takashi Ebihara, Shizufumi Mori, Kentaro Yokota, Yoshifumi Shigeyoshi, Yasufumi Kinki Univ Dept Anat & Neurobiol Sch Med Osaka 5898511 Japan RIKEN Brain Sci Inst Lab Mental Biol Wako Saitama 3510198 Japan Nagoya Univ Grad Sch Bioagr Sci Physiol Anim Lab Dept Appl Mol BiosciChikusa Ku Nagoya Aichi 4648601 Japan Nagoya Univ Grad Sch Bioagr Sci Div Biomodeling Chikusa Ku Nagoya Aichi 4648601 Japan Univ Fukui Div Mol Genet Dept Biochem & Bioinformat Sci Fac Med Sci Fukui 9101193 Japan

The mammalian circadian oscillator is composed of interacting positive and negative transcription events. The clock proteins PER1 and PER2 play essential roles in a negative limb of the feedback loop that generates the circadian rhythm in mammals. In addition, the proteins CLOCK and BMAL1 (also known as ARNTL) form a heterodimer that drives the Per genes via the E-box consensus sequences within their promoter regions. In the present study, we demonstrate that Id2 is involved in stabilization of the amplitudes of the circadian oscillations by suppressing transcriptional activation of clock genes Clock and Bmal1. Id2 shows dynamic oscillation in the SCN, with a peak in the late subjective night. Under constant dark conditions (DD), Id2(-/-) mice showed no apparent difference in locomotor activity, however, under constant light conditions (LL), Id2(-/-) mice exhibit aberrant locomotor activity, with lower circadian oscillation amplitudes, although the free running periods in Id2(-/-) mice show no differences from those in either wild type or heterozygous mice. Id2(-/-) animals also exhibit upregulation of Per1 in constant light, during both the subjective night and day. In wild type mice, Id2 is upregulated by constant light exposure during the subjective night. We propose that Id2 expression in the SCN contributes to maintenance of dynamic circadian oscillations.

关键词： circadian rhythm Id2 Per1 basic helix-loop-helix constant light conditions

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SRY Induced TCF21 Genome-Wide Targets and Cascade of bHLH Factors During Sertoli Cell Differentiation and Male Sex Determination in Rats

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BIOLOGY OF REPRODUCTION 2012年第6期87卷 null-null页

作者： Bhandari, Ramji K. Schinke, Ellyn N. Haque, Md. M. Sadler-Riggleman, Ingrid Skinner, Michael K. Washington State Univ Ctr Reprod Biol Sch Biol Sci Pullman WA 99164 USA

Male sex determination is initiated through the testis-determining factor SRY that promotes Sertoli cell differentiation and subsequent gonadal development. The basic helix-loop-helix (bHLH) gene Tcf21 was identified as one of the direct downstream targets of SRY. The current study was designed to identify the downstream targets of TCF21 and the potential cascade of bHLH genes that promote Sertoli cell differentiation. A modified ChIP-Chip comparative hybridization analysis identified 121 direct downstream binding targets for TCF21. The gene networks and cellular pathways potentially regulated by these TCF21 targets were identified. One of the main bHLH targets for TCF21 was the bHLH gene scleraxis (Scx). An embryonic ovarian gonadal cell culture was used to examine the functional role of Sry, Tcf21, and Scx to promote an in vitro sex reversal and induction of Sertoli cell differentiation. SRY and TCF21 were found to induce the initial stages of Sertoli cell differentiation, whereas SCX was found to induce the later stages of Sertoli cell differentiation associated with pubertal development using transferrin gene expression as a marker. Therefore, a cascade of SRY followed by TCF21 followed by SCX appears to promote, in part, Sertoli cell fate determination and subsequent differentiation. The current observations help elucidate the initial molecular events involved in the induction of Sertoli cell differentiation and testis development.

关键词： basic helix-loop-helix cell differentiation ChIP-Chip SRY scleraxis Scx Sertoli cells sex determination testis development

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Interaction with plant transcription factors can mediate nuclear import of phytochrome B

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 2012年第15期109卷 5892-5897页

作者： Pfeiffer, Anne Nagel, Marie-Kristin Popp, Claudia Wuest, Florian Bindics, Janos Viczian, Andras Hiltbrunner, Andreas Nagy, Ferenc Kunkel, Tim Schaefer, Eberhard Univ Freiburg Fac Biol D-79104 Freiburg Germany Univ Freiburg Ctr Biol Signalling Studies D-79104 Freiburg Germany Inst Plant Biol Biol Res Ctr H-6726 Szeged Hungary Univ Tubingen Ctr Plant Mol Biol D-72076 Tubingen Germany Univ Edinburgh Sch Biol Sci Edinburgh EH9 3JH Midlothian Scotland

Phytochromes (phy) are red/far-red-absorbing photoreceptors that regulate the adaption of plant growth and development to changes in ambient light conditions. The nuclear transport of the phytochromes upon light activation is regarded as a key step in phytochrome signaling. Although nuclear import of phyA is regulated by the transport facilitators far red elongated hypocotyl 1 (FHY1) and fhy1-like, an intrinsic nuclear localization signal was proposed to be involved in the nuclear accumulation of phyB. We recently showed that nuclear import of phytochromes can be analyzed in a cell-free system consisting of isolated nuclei of the unicellular green algae Acetabularia acetabulum. We now show that this system is also versatile to elucidate the mechanism of the nuclear transport of phyB. We tested the nuclear transport characteristics of full-length phyB as well as N-and C-terminal phyB fragments in vitro and showed that the nuclear import of phyB can be facilitated by phytochrome-interacting factor 3 (PIF3). In vivo measurements of phyB nuclear accumulation in the absence of PIF1, -3, -4, and -5 indicate that these PIFs are the major transport facilitators during the first hours of deetiolation. Under prolonged irradiations additional factors might be responsible for phyB nuclear transport in the plant.

关键词： Arabidopsis basic helix-loop-helix signal transduction

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basic helix-loop-helix transcription factor profiling of lung tumors shows aberrant expression of the proneural gene atonal homolog 1 (ATOH1, HATH1, MATH1) in neuroendocrine tumors

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INTERNATIONAL JOURNAL OF BIOLOGICAL MARKERS 2007年第2期22卷 114-123页

作者： Westerman, B. A. Breuer, R. H. J. Poutsma, A. Chhatta, A. Noorduyn, L. A. Koolen, M. G. J. Postmus, P. E. Blankenstein, M. A. Oudejans, C. B. M. Vrije Univ Amsterdam Med Ctr Mol Biol Lab Dept Clin Chem NL-1007 MB Amsterdam Netherlands Vrije Univ Amsterdam Med Ctr Dept Pulmonol NL-1007 MB Amsterdam Netherlands Univ Amsterdam Acad Med Ctr Dept Pathol NL-1105 AZ Amsterdam Netherlands Univ Amsterdam Acad Med Ctr Dept Pulmonol NL-1105 AZ Amsterdam Netherlands

Microarray-based expression profiling studies of lung adenocarcinomas have defined neuroendocrine subclasses with poor prognosis. As neuroendocrine development is regulated by members of the achaete-scute and atonal classes of basic helix-loop-helix (bHLH) transcription factors, we analyzed lung tumors for expression of these factors. Out of 13 bHLH genes tested, 4 genes, i.e., achaete-scute complex-like 1 (ASCL1, HASH1, Mash1), atonal homolog 1 (ATOH1, HATH1, MATH1), NEUROD4 (ATH-3, Atoh3, MATH-3) and neurogenic differentiation factor 1 (NEUROD1, NEUROD, BETA2), showed differential expression among lung tumors and absent or low expression in normal lung. As expected, tumors that have high levels of ASCL1 also express neuroendocrine markers, and we found that this is accompanied by increased levels of NEUROD1. In addition, we found ATOH1 expression in 9 (16%) out of 56 analyzed adenocarcinomas and these tumors showed neuroendocrine features as shown by dopa decarboxylase mRNA expression and immunostaining for neuroendocrine markers. ATOH1 expression as well as NEUROD4 was observed in small cell lung carcinoma (SCLC), a known neuroendocrine tumor. Since ATOH1 is not known to be involved in normal lung development, our results suggest that aberrant activation of ATOH1 leads to a neuroendocrine phenotype similar to what is observed for ASCL1 activation during normal neuroendocrine development and in lung malignancies. Our preliminary data indicate that patients with ATOH1-expressing adenocarcinomas might have a worse prognosis.

关键词： lung cancer basic helix-loop-helix transcription factor

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