Identification of genes differentially expressed in a strain of the moldAspergillus nidulanscarrying a loss-of-function mutation in thepalAgene

2008 ◽  
Vol 54 (10) ◽  
pp. 803-811 ◽  
Author(s):  
Emiliana M. Silva ◽  
Janaína S. Freitas ◽  
Diana E. Gras ◽  
Fábio M. Squina ◽  
Juliana Leal ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Stress Responses ◽  
Genome Stability ◽  
Sugar Content ◽  
Signal Transduction Pathway ◽  
Subtractive Hybridization ◽  
Differentially Expressed ◽  
Neutral Sugar ◽  
Loss Of Function ◽  
Secretion Signal

To identify genes differentially expressed in a strain of the mold Aspergillus nidulans carrying a loss-of-function mutation in palA, a gene in the pH-responsive signal transduction pathway, suppression subtractive hybridization was performed between RNA isolated from the biA1 and biA1 palA1 strains grown under limiting inorganic phosphate at pH 5.0. We have identified several genes upregulated in the biA1 palA1 mutant strain that play important roles in mitotic fidelity, stress responses, enzyme secretion, signal transduction mechanisms, development, genome stability, phosphate sensing, and transcriptional regulation among others. The upregulation of eight of these transcripts was also validated by Northern blot. Moreover, we show that a loss of function mutation in the palA gene drastically reduced the neutral sugar content of the acid phosphatase PacA secreted by the fungus A. nidulans grown at pH 5.0 compared with a control strain.

scholarly journals Further Characterization of the Signaling Proteolysis Step in the Aspergillus nidulans pH Signal Transduction Pathway

2007 ◽  
Vol 6 (6) ◽  
pp. 960-970 ◽  
Author(s):  
María M. Peñas ◽  
América Hervás-Aguilar ◽  
Tatiana Múnera-Huertas ◽  
Elena Reoyo ◽  
Miguel Á. Peñalva ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Aspergillus Nidulans ◽  
Cysteine Protease ◽  
Mutational Analysis ◽  
Signal Transduction Pathway ◽  
Missense Mutations ◽  
Loss Of Function ◽  
Western Blots ◽  
C Terminus ◽  
Catalytic Cysteine

ABSTRACT The Aspergillus nidulans pH-responsive transcription factor PacC is modulated by limited, two-step proteolysis. The first, pH-regulated cleavage occurs in the 24-residue highly conserved “signaling protease box” in response to the alkaline pH signal. This is transduced by the Pal signaling pathway, containing the predicted calpain-like cysteine protease and likely signaling protease, PalB. In this work, we carried out classical mutational analysis of the putative signaling protease PalB, and we describe 9 missense and 18 truncating loss-of-function (including null) mutations. Mutations in the region of and affecting directly the predicted catalytic cysteine strongly support the deduction that PalB is a cysteine protease. Truncating and missense mutations affecting the C terminus highlight the importance of this region. Analysis of three-hemagglutinin-tagged PalB in Western blots demonstrates that PalB levels are independent of pH and Pal signal transduction. We have followed the processing of MYC3-tagged PacC in Western blots. We show unequivocally that PalB is essential for signaling proteolysis and is definitely not the processing protease. In addition, we have replaced 15 residues of the signaling protease box of MYC3-tagged PacC (pacC900) with alanine. The majority of these substitutions are silent. Leu481Ala, Tyr493Ala, and Gln499Ala result in delayed PacC processing in response to shifting from acidic to alkaline medium, as determined by Western blot analysis. Leu498Ala reduces function much more markedly, as determined by plate tests and processing recalcitrance. Excepting Leu498, this demonstrates that PacC signaling proteolysis is largely independent of sequence in the cleavage region.

scholarly journals Full-length transcriptome sequencing of the identified fruit shape-related genes of the Olecranon honey peach

2020 ◽  
Author(s):  
Jianliang Liu ◽  
Yao Bao ◽  
Qin Wang ◽  
Huifan Liu
Keyword(s):  
Signal Transduction ◽  
Transcriptome Sequencing ◽  
Signal Transduction Pathway ◽  
Fruit Shape ◽  
Full Length ◽  
Differentially Expressed ◽  
Expression Of Genes ◽  
Mutant Variant ◽  
Oxford Nanopore ◽  
New Gene

Abstract Background: The olecranon honey peach belongs to the peach class. In terms of the fruit type, the Olecranon honey peach, shaped like an eagle’s beak, is larger than others. In this study, Full-length transcriptome sequencing of the Olecranon honey peach and the bud mutant variant of the peach was performed by Oxford Nanopore Technologies to comparatively analyze the differentially expressed genes and the transcriptome, to identify important fruit shape-related genes.Results:Full-length transcriptome sequencing was performed to analyze the two peaches. Consensus isoform was obtained and compared to the reference genome for a de-redundancy analysis. As a result, a final set of 58,596 transcript sequences was obtained. A total of 21,745 simple sequence repeats were obtained, and 18,322 alternative splicing (AS) events were identified. The comparative analysis of the non-redundant transcript revealed 2530 new gene loci and 37,364 novel transcripts. A total of 457 genes were differentially expressed in the two groups, including 169 up-regulated genes and 288 down-regulated genes. A total of 1519 transcripts were differentially expressed, of which 552 were up-regulated and 997 were down-regulated. Conclusions: In the case of the plant hormone signal transduction pathway, identified by the KEGG annotation, our analyses revealed that differential expression of genes 9229, 26004, 22504, 2822, 2826, 2824, ONT.1953, ONT.1950, and ONT.1953 was related to the shape of the peach and may regulate the production of large fruits, via endogenous hormones, secondary metabolites, and signal transduction. This study provided useful information on the shape-related genes and transcripts in the Olecranon honey peach.

scholarly journals A Ras-mediated signal transduction pathway is involved in the control of sex myoblast migration in Caenorhabditis elegans

Development ◽  
1996 ◽  
Vol 122 (9) ◽  
pp. 2823-2833 ◽  
Author(s):  
M. Sundaram ◽  
J. Yochem ◽  
M. Han
Keyword(s):  
Signal Transduction ◽  
Caenorhabditis Elegans ◽  
Growth Factor Receptor ◽  
Signal Transduction Pathway ◽  
Body Region ◽  
Transduction Pathway ◽  
Loss Of Function ◽  
Ras Pathway ◽  
Mosaic Analysis ◽  
Sex Myoblasts

Sex myoblast migration in the Caenorhabditis elegans hermaphrodite represents a simple, genetically amenable model system for studying how cell migration is regulated during development. Two separable components of sex myoblast guidance have been described: a gonad-independent mechanism sufficient for the initial anterior migration to the mid-body region, and a gonad-dependent mechanism required for precise final positioning (J. H. Thomas, M. J. Stern and H. R. Horvitz (1990) Cell 62, 1041–1052). Here, we demonstrate a role for a Ras-mediated signal transduction pathway in controlling sex myoblast migration. Loss-of-function mutations in let-60 ras, ksr-1, lin-45 raf, let-537/mek-2 or sur-1/mpk-1 cause defects in sex myoblast final positions that resemble those seen in gonad-ablated animals, while constitutively active let-60 ras(G13E) trans-genes allow fairly precise positioning to occur in the absence of the gonad. A mosaic analysis demonstrated that let-60 ras is required within the sex myoblasts to control proper positioning. Our results suggest that gonadal signals normally stimulate let-60 ras activity in the sex myoblasts, thereby making them competent to sense or respond to positional cues that determine the precise endpoint of migration. let-60 ras may have additional roles in sex myoblast guidance as well. Finally, we have also investigated genetic interactions between let-60 ras and other genes important for sex myoblast migration, including egl-15, which encodes a fibroblast growth factor receptor tyrosine kinase (D. L. DeVore, H. R. Horvitz and M. J. Stern (1995) Cell 83, 611–623). Since mutations reducing Ras pathway activity cause a different phenotype than those reducing egl-15 activity and since constitutive Ras activity only partially suppresses the migration defects of egl-15 mutants, we argue that let-60 ras and egl-15 do not act together in a single linear pathway.

Full-length transcriptome sequencing of the identified fruit shape-related genes of the Olecranon honey peach

2020 ◽  
Author(s):  
Jianliang Liu ◽  
Yao Bao ◽  
Qin Wang ◽  
Huifan Liu
Keyword(s):  
Signal Transduction ◽  
Transcriptome Sequencing ◽  
Signal Transduction Pathway ◽  
Fruit Shape ◽  
Full Length ◽  
Differentially Expressed ◽  
Expression Of Genes ◽  
Mutant Variant ◽  
Oxford Nanopore ◽  
New Gene

Abstract Background: The Olecranon honey peach shaped like an eagle’s beak. In this study, full-length transcriptome sequencing of the Olecranon honey peach and its bud mutant variant was performed by Oxford Nanopore Technologies to comparatively analyze the differentially expressed genes and the transcriptome to identify important fruit shape-related genes. Results: Full-length transcriptome sequencing was performed to analyze the two peaches. A consensus isoform was obtained and compared to the reference genome for an elimination of redundancy analysis. As a result, a final set of 58 596 transcript sequences was obtained. A total of 21 745 simple sequence repeats were obtained, and 18 322 alternative splicing (AS) events were identified. The comparative analysis of the non-redundant transcript revealed 2530 new gene loci and 37 364 novel transcripts. A total of 457 genes were differentially expressed in the two groups, including 169 up-regulated genes and 288 down-regulated genes. A total of 1519 transcripts were differentially expressed, of which 552 were up-regulated and 997 were down-regulated. Conclusions: In the case of the plant hormone signal transduction pathway identified by the KEGG annotation, our analyses revealed that differential expression of genes 9229 , 26004 , 22504 , 2822 , 2826 , 2824 , ONT.1953 , ONT.1950 , and ONT.1953 was related to the shape of the peach and may regulate the production of large fruit, via endogenous hormones, secondary metabolites, and signal transduction. This study provides useful information on the shape-related genes and transcripts in the Olecranon honey peach.

scholarly journals MAPK Signal Transduction Pathway Regulation: A Novel Mechanism of Rat HSC-T6 Cell Apoptosis Induced by FUZHENGHUAYU Tablet

2013 ◽  
Vol 2013 ◽  
pp. 1-13 ◽  
Author(s):  
Qi Wang ◽  
Hongbo Du ◽  
Min Li ◽  
Yue Li ◽  
Shunai Liu ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Target Genes ◽  
Stellate Cell ◽  
Signal Transduction Pathway ◽  
Differentially Expressed ◽  
Mrna Levels ◽  
Protein Levels ◽  
Control Serum ◽  
Pathway Regulation ◽  
Induced Apoptosis

FUZHENGHUAYU Tablets have been widely used in the treatment of liver fibrosis in China. Here, we investigate the apoptotic effect of FUZHENGHUAYU Tablet in rat liver stellate cell line HSC-T6. HSC-T6 cells were incubated with control serum or drug serum from rats fed with 0.9% NaCl or FUZHENGHUAYU Tablet, respectively. Cells exposed to drug serum showed higher proportions of early and late apoptotic cells than controls. The mRNA levels of collagens I and III, TGF-β1 andα-SMA were reduced by drug serum compared to control serum. Differentially expressed mRNAs and miRNAs were analyzed by microarray and sequencing, respectively. We identified 334 differentially expressed mRNAs and also 60 GOs and two pathways related to the mRNAs. Seventy-five differentially expressed miRNAs were down-regulated by drug serum and 1963 target genes were predicted. 134 GOs up-regulated in drug serum group were linked to miRNA targets, and drug serum also regulated 43 miRNA signal transduction pathways. Protein levels were evaluated by Western blot. Drug serum down-regulated (phospho-SAPK/JNK)/(SAPK/JNK) and up-regulated phospho-p38/p38 ratios. The study showed that FUZHENGHUAYU Tablet induced apoptosis in rat HSC-T6 cells possibly in part by activating p38 and inhibiting SAPK/JNK.

scholarly journals Deep Sequencing of Small RNA Reveals the Molecular Regulatory Network of AtENO2 Regulating Seed Germination

2021 ◽  
Vol 22 (10) ◽  
pp. 5088
Author(s):  
Yu Wu ◽  
Lamei Zheng ◽  
Jie Bing ◽  
Huimin Liu ◽  
Genfa Zhang
Keyword(s):  
Signal Transduction ◽  
Seed Germination ◽  
Deep Sequencing ◽  
Small Rna ◽  
Stress Responses ◽  
Target Genes ◽  
Differentially Expressed ◽  
Signal Transduction Pathways ◽  
Go Annotation ◽  
Differentially Expressed Mirnas

Seed germination is a key step in the new life cycle of plants. In agriculture, we regard the rapid and consistent process of seed germination as one of the necessary conditions to measure the high quality and yield of crops. ENO2 is a key enzyme in glycolysis, which also plays an important role in plant growth and abiotic stress responses. In our study, we found that the time of seed germination in AtENO2 mutation (eno2−) was earlier than that of wild type (WT) in Arabidopsis thaliana. Previous studies have shown that microRNAs (miRNAs) were vital in seed germination. After deep sequencing of small RNA, we found 590 differentially expressed miRNAs in total, of which 87 were significantly differentially expressed miRNAs. By predicting the target genes of miRNAs and analyzing the GO annotation, we have counted 18 genes related to seed germination, including ARF family, TIR1, INVC, RR19, TUDOR2, GA3OX2, PXMT1, and TGA1. MiR9736-z, miR5059-z, ath-miR167a-5p, ath-miR167b, ath-miR5665, ath-miR866-3p, miR10186-z, miR8165-z, ath-miR857, ath-miR399b, ath-miR399c-3p, miR399-y, miR163-z, ath-miR393a-5p, and ath-miR393b-5p are the key miRNAs regulating seed germination-related genes. Through KEGG enrichment analysis, we found that phytohormone signal transduction pathways were significantly enriched, and these miRNAs mentioned above also participate in the regulation of the genes in plant hormone signal transduction pathways, thus affecting the synthesis of plant hormones and further affecting the process of seed germination. This study laid the foundation for further exploration of the AtENO2 regulation for seed germination.

scholarly journals Biochemical analysis of torso and D-raf during Drosophila embryogenesis: implications for terminal signal transduction.

1993 ◽  
Vol 13 (2) ◽  
pp. 1163-1172 ◽  
Author(s):  
F Sprenger ◽  
M M Trosclair ◽  
D K Morrison
Keyword(s):  
Signal Transduction ◽  
Tyrosine Kinase ◽  
Biochemical Analysis ◽  
Kinase Activity ◽  
Signal Transduction Pathway ◽  
Egg Laying ◽  
Loss Of Function ◽  
Tyrosine Kinase Activity ◽  
Phosphorylation State ◽  
Drosophila Embryos

Determination of anterior and posterior terminal structures of Drosophila embryos requires activation of two genes encoding putative protein kinases, torso and D-raf. In this study, we demonstrate that Torso has intrinsic tyrosine kinase activity and show that it is transiently tyrosine phosphorylated (activated) at syncytial blastoderm stages. Torso proteins causing a gain-of-function phenotype are constitutively tyrosine phosphorylated, while Torso proteins causing a loss-of-function phenotype lack tyrosine kinase activity. The D-raf gene product, which is required for Torso function, is identified as a 90-kDa protein with intrinsic serine/threonine kinase activity. D-Raf is expressed throughout embryogenesis; however, the phosphorylation state of the protein changes during development. In wild-type embryos, D-Raf is hyperphosphorylated at 1 to 2 h after egg laying, and thereafter only the most highly phosphorylated form is detected. Embryos lacking Torso activity, however, show significant reductions in D-Raf protein expression rather than major alterations in the protein's phosphorylation state. This report provides the first biochemical analysis of the terminal signal transduction pathway in Drosophila embryos.

scholarly journals The ATR-WEE1 kinase module inhibits the MAC complex to regulate replication stress response

2021 ◽  
Vol 49 (3) ◽  
pp. 1411-1425 ◽  
Author(s):  
Lili Wang ◽  
Li Zhan ◽  
Yan Zhao ◽  
Yongchi Huang ◽  
Chong Wu ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Stress Responses ◽  
Genome Stability ◽  
Intron Retention ◽  
Cell Cycle Control ◽  
Replication Stress ◽  
Loss Of Function ◽  
Evolutionarily Conserved ◽  
Subsequent Degradation ◽  
Wee1 Kinase

Abstract DNA damage response is a fundamental mechanism to maintain genome stability. The ATR-WEE1 kinase module plays a central role in response to replication stress. Although the ATR-WEE1 pathway has been well studied in yeasts and animals, how ATR-WEE1 functions in plants remains unclear. Through a genetic screen for suppressors of the Arabidopsis atr mutant, we found that loss of function of PRL1, a core subunit of the evolutionarily conserved MAC complex involved in alternative splicing, suppresses the hypersensitivity of atr and wee1 to replication stress. Biochemical studies revealed that WEE1 directly interacts with and phosphorylates PRL1 at Serine 145, which promotes PRL1 ubiquitination and subsequent degradation. In line with the genetic and biochemical data, replication stress induces intron retention of cell cycle genes including CYCD1;1 and CYCD3;1, which is abolished in wee1 but restored in wee1 prl1. Remarkably, co-expressing the coding sequences of CYCD1;1 and CYCD3;1 partially restores the root length and HU response in wee1 prl1. These data suggested that the ATR-WEE1 module inhibits the MAC complex to regulate replication stress responses. Our study discovered PRL1 or the MAC complex as a key downstream regulator of the ATR-WEE1 module and revealed a novel cell cycle control mechanism.

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