Structure-function analysis of the EGF-CFC family member Cripto identifies residues essential for nodal signalling

Development ◽  
2001 ◽  
Vol 128 (22) ◽  
pp. 4501-4510
Author(s):  
Gabriella Minchiotti ◽  
Giuseppe Manco ◽  
Silvia Parisi ◽  
Carmine T. Lago ◽  
Frederic Rosa ◽  
...  
Keyword(s):  
Structural Model ◽  
Function Analysis ◽  
Three Dimensional ◽  
Point Mutations ◽  
Amino Acid Residues ◽  
Vertebrate Development ◽  
Loss Of Function ◽  
Protein Protein Interaction ◽  
Functional Relevance

cripto is the founding member of the family of EGF-CFC genes, a class of extracellular factors essential for early vertebrate development. In this study we show that injection of Cripto recombinant protein in mid to late zebrafish Maternal-Zygotic one-eyed pinhead (MZoep) blastulae was able to fully rescue the mutant phenotype, thus providing the first direct evidence that Cripto activity can be added extracellularly to recover oep-encoded function in zebrafish early embryos. Moreover, 15 point mutations and two deletion mutants were generated to assess in vivo their functional relevance by comparing the ability of cripto wild-type and mutant RNAs to rescue the zebrafish MZoep mutant. From this study we concluded that the EGF-CFC domain is sufficient for Cripto biological activity and identified ten point mutations with a functional defective phenotype, two of which, located in the EGF-like domain, correspond to loss-of-function mutations. Finally, we have developed a three-dimensional structural model of Cripto protein and used it as a guide to predict amino acid residues potentially implicated in protein-protein interaction.

scholarly journals Proteins and Molecular Pathways Relevant for the Malignant Properties of Tumor-Initiating Pancreatic Cancer Cells

Cells ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 1397
Author(s):  
Lisa Samonig ◽  
Andrea Loipetzberger ◽  
Constantin Blöchl ◽  
Marc Rurik ◽  
Oliver Kohlbacher ◽  
...  
Keyword(s):  
Calcium Binding ◽  
Function Analysis ◽  
Critical Role ◽  
Three Dimensional ◽  
Small Subset ◽  
Loss Of Function ◽  
Tumor Initiating Cells ◽  
Differential Proteomics ◽  
Pancreatic Cancer Cells

Cancer stem cells (CSCs), a small subset of the tumor bulk with highly malignant properties, are deemed responsible for tumor initiation, growth, metastasis, and relapse. In order to reveal molecular markers and determinants of their tumor-initiating properties, we enriched rare stem-like pancreatic tumor-initiating cells (TICs) by harnessing their clonogenic growth capacity in three-dimensional multicellular spheroid cultures. We compared pancreatic TICs isolated from three-dimensional tumor spheroid cultures with nontumor-initiating cells (non-TICs) enriched in planar cultures. Employing differential proteomics (PTX), we identified more than 400 proteins with significantly different expression in pancreatic TICs and the non-TIC population. By combining the unbiased PTX with mRNA expression analysis and literature-based predictions of pro-malignant functions, we nominated the two calcium-binding proteins S100A8 (MRP8) and S100A9 (MRP14) as well as galactin-3-binding protein LGALS3BP (MAC-2-BP) as putative determinants of pancreatic TICs. In silico pathway analysis followed by candidate-based RNA interference mediated loss-of-function analysis revealed a critical role of S100A8, S100A9, and LGALS3BP as molecular determinants of TIC proliferation, migration, and in vivo tumor growth. Our study highlights the power of combining unbiased proteomics with focused gene expression and functional analyses for the identification of novel key regulators of TICs, an approach that warrants further application to identify proteins and pathways amenable to drug targeting.

scholarly journals Identification of Amino Acid Residues within Simian Virus 40 Capsid Proteins Vp1, Vp2, and Vp3 That Are Required for Their Interaction and for Viral Infection

2006 ◽  
Vol 80 (18) ◽  
pp. 8891-8898 ◽  
Author(s):  
Akira Nakanishi ◽  
Akiko Nakamura ◽  
Robert Liddington ◽  
Harumi Kasamatsu
Keyword(s):  
Structural Model ◽  
Simian Virus 40 ◽  
Simian Virus ◽  
Capsid Proteins ◽  
Amino Acid Residues ◽  
Sequence Elements ◽  
Capsid Protein Vp1 ◽  
Necessary And Sufficient

ABSTRACT Interaction of simian virus 40 (SV40) major capsid protein Vp1 with the minor capsid proteins Vp2 and Vp3 is an integral aspect of the SV40 architecture. Two Vp3 sequence elements mediate Vp1 pentamer binding in vitro, Vp3 residues 155 to 190, or D1, and Vp3 residues 222 to 234, or D2. Of the two, D1 but not D2 was necessary and sufficient to direct the interaction with Vp1 in vivo. Rational mutagenesis of Vp3 residues (Phe157, Ile158, Pro164, Gly165, Gly166, Leu177, and Leu181) or Vp1 residues (Val243 and Leu245), based on a structural model of the SV40 Vp1 pentamer complexed with Vp3 D1, was carried out to disrupt the interaction between Vp1 and Vp3 and to study the consequences of these mutations for viral viability. Altering these residues to bulky, charged residues blocked the interaction in vitro. When these alterations were introduced into the viral genome, they reduced viral viability. Mutants with alterations in Vp1 Val243, Leu245, or both to glutamate were nearly nonviable, whereas those with Vp3 alterations reduced, but did not eliminate, viability. Our results defined the residues of Vp1 and the minor capsid proteins that are essential for both the interaction of the capsid proteins and viral viability in permissive cells.

scholarly journals Loss-of-Function Analysis Suggests That Omi/HtrA2 Is Not an Essential Component of the pink1/parkin Pathway In Vivo

2008 ◽  
Vol 28 (53) ◽  
pp. 14500-14510 ◽  
Author(s):  
J. Yun ◽  
J. H. Cao ◽  
M. W. Dodson ◽  
I. E. Clark ◽  
P. Kapahi ◽  
...  
Keyword(s):  
Function Analysis ◽  
Loss Of Function ◽  
Essential Component

Structure - function analysis of photosystem II subunit S (PsbS) in vivo

2002 ◽  
Vol 29 (10) ◽  
pp. 1131 ◽  
Author(s):  
Xiao-Ping Li ◽  
Alba Phippard ◽  
Jae Pasari ◽  
Krishna K. Niyogi
Keyword(s):  
Amino Acid ◽  
Photosystem Ii ◽  
Function Analysis ◽  
Amino Acid Sequences ◽  
Forward Genetics ◽  
Photochemical Quenching ◽  
Amino Acid Residues ◽  
The Stability ◽  
Psbs Gene

In land plants, photosystem II subunit S (PsbS) plays a key role in xanthophyll- and pH-dependent non-photochemical quenching (qE) of excess absorbed light energy. Arabidopsis thaliana (L.) Heynh. npq4 mutants are defective in the psbS gene and have impaired qE. Exactly how the PsbS protein is involved in qE is unclear, but it has been proposed that PsbS binds H+ and/or de-epoxidized xanthophylls in excess light as part of the qE mechanism. To identify amino acid residues that are important for PsbS function, we sequenced the psbS gene from eight npq4 point mutant alleles isolated by forward genetics screening, including two new alleles. In the four transmembrane helices of PsbS, several amino acid residues were found to affect the stability and/or function of the protein. By comparing the predicted amino acid sequences of PsbS from several plant species and studying the proposed topological structure of PsbS, eight possible H+-binding amino acid residues on the lumenal side of the protein were identified and then altered by site-directed mutagenesis in vitro. The mutant psbS genes were transformed into npq4-1, a psbS deletion mutant, to test the stability and function of the mutant PsbS proteins in�vivo. The results demonstrate that two conserved, protonatable amino acids, E122 and E226, are especially critical for the function of PsbS.

scholarly journals Substrate (aglycone) specificity of human cytosolic beta-glucosidase

2003 ◽  
Vol 373 (1) ◽  
pp. 41-48 ◽  
Author(s):  
Jean-Guy BERRIN ◽  
Mirjam CZJZEK ◽  
Paul A. KROON ◽  
W. Russell MCLAUCHLAN ◽  
Antoine PUIGSERVER ◽  
...  
Keyword(s):  
Structural Model ◽  
Homology Modelling ◽  
Three Dimensional ◽  
Amino Acid Residues ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
Mutant Proteins ◽  
Metabolizing Enzyme ◽  
Beta Glucosidase

Human cytosolic β-glucosidase (hCBG) is a xenobiotic-metabolizing enzyme that hydrolyses certain flavonoid glucosides, with specificity depending on the aglycone moiety, the type of sugar and the linkage between them. Based upon the X-ray structure of Zea mays β-glucosidase, we generated a three-dimensional model of hCBG by homology modelling. The enzyme exhibited the (β/α)8-barrel fold characteristic of family 1 β-glucosidases, with structural differences being confined mainly to loop regions. Based on the substrate specificity of the human enzymes, sequence alignment of family 1 enzymes and analysis of the hCBG structural model, we selected and mutated putative substrate (aglycone) binding site residues. Four single mutants (Val168→Tyr, Phe225→Ser, Tyr308→Ala and Tyr308→Phe) were expressed in Pichia pastoris, purified and characterized. All mutant proteins showed a decrease in activity towards a broad range of substrates. The Val168→Tyr mutation did not affect Km on p-nitrophenyl (pNP)-glycosides, but increased Km 5-fold on flavonoid glucosides, providing the first biochemical evidence supporting a role for this residue in aglycone-binding of the substrate, a finding consistent with our three-dimensional model. The Phe225→Ser and Tyr308→Ala mutations, and, to a lesser degree, the Tyr308→Phe mutation, resulted in a drastic decrease in specific activities towards all substrates tested, indicating an important role of those residues in catalysis. Taken together with the three-dimensional model, these mutation studies identified the amino-acid residues in the aglycone-binding subsite of hCBG that are essential for flavonoid glucoside binding and catalysis.

scholarly journals Loss offlflTriggers JNK-Dependent Cell Death inDrosophila

2015 ◽  
Vol 2015 ◽  
pp. 1-8 ◽  
Author(s):  
Jiuhong Huang ◽  
Lei Xue
Keyword(s):  
Cell Death ◽  
Function Analysis ◽  
Ectopic Expression ◽  
Negative Regulator ◽  
Loss Of Function ◽  
Jnk Pathway ◽  
Dependent Cell ◽  
Jnk Activation ◽  
First Time

falafel(flfl) encodes aDrosophilahomolog of human SMEK whosein vivofunctions remain elusive. In this study, we performed gain-of-function and loss-of-function analysis inDrosophilaand identified flfl as a negative regulator of JNK pathway-mediated cell death. While ectopic expression offlflsuppresses TNF-triggered JNK-dependent cell death, loss offlflpromotes JNK activation and cell death in the developing eye and wing. These data report for the first time an essential physiological function offlflin maintaining tissue homeostasis and organ development. As the JNK signaling pathway has been evolutionary conserved from fly to human, a similar role of PP4R3 in JNK-mediated physiological process is speculated.

scholarly journals Codon optimality is the primary contributor to the exceptional mutational sensitivity of CcdA antitoxin in its operonic context

2022 ◽  
Author(s):  
Soumyanetra Chandra ◽  
Kritika Gupta ◽  
Shruti Khare ◽  
Pehu Kohli ◽  
Aparna Asok ◽  
...  
Keyword(s):  
Large Fraction ◽  
Point Mutations ◽  
Saturation Mutagenesis ◽  
Loss Of Function ◽  
Active Site Residues ◽  
Synonymous Mutations ◽  
Protein Levels ◽  
Intrinsically Disordered ◽  
Usage Frequency

Deep mutational scanning studies suggest that single synonymous mutations are typically silent and that most exposed, non active-site residues are tolerant to mutations. Here we show that the ccdA antitoxin component of the E.coli ccdAB toxin-antitoxin operonic system is unusually sensitive to mutations when studied in the operonic context. A large fraction (~80%) of single codon mutations, including many synonymous mutations in the ccdA gene show inactive phenotypes that are correlated with the E.coli codon usage frequency but retain native-like binding affinity towards cognate toxin, CcdB. Therefore, the observed phenotypic effects are largely not due to alterations in protein structure or stability, consistent with the fact that a large region of CcdA is intrinsically disordered. In select cases, proteomics studies reveal altered ratios of CcdA:CcdB protein levels in vivo, suggesting that these mutations likely alter relative translation efficiencies of the two genes in the operon. We extend these results by predicting and validating single synonymous mutations that lead to loss of function phenotypes in the relBE operon upon introduction of rarer codons. Thus, in their native context, genes are likely to be more sensitive to both synonymous and non-synonymous point mutations than inferred from previous saturation mutagenesis studies.

scholarly journals TCN1 Deficiency Inhibits The Malignancy of Colorectal Cancer Cells By Regulating The ITGB4 Pathway

2021 ◽  
Author(s):  
Xinqiang Zhu ◽  
Xuetong Jiang ◽  
Qinglin Zhang ◽  
Hailong Huang ◽  
Xiaohong Shi ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Molecular Mechanisms ◽  
Function Analysis ◽  
Hct116 Cell ◽  
Tumor Xenograft ◽  
Integrin Subunit ◽  
Filamin A ◽  
Loss Of Function ◽  
Colorectal Cancer Cells

Abstract Background: This study aimed to investigate the biological function and regulatory mechanism of TCN1 in colorectal cancer (CRC). Methods: We studied the biological functions of TCN1 using gain-of-function and loss-of-function analysis in HCT116 cell lines, and examined the effects of TCN1 on the proliferation, apoptosis, and invasion of CRC cells and determined its potential molecular mechanisms using CRC lines and mouse xenotransplantation models. Tumor xenograft and tumor metastasis studies were performed to detect the tumorigenicity and metastasis of cells in vivo. Results: TCN1-knockdown attenuated CRC cell proliferation, invasion and promoted cell apoptosis. Overexpression of TCN1 yielded the opposite effects. In addition, TCN1-knockdown HCT116 cells failed to form metastatic foci in the peritoneum after intravenous injection. Molecular mechanism studies showed that TCN1 interacts with integrin subunit β4 (ITGB4) to positively regulate the expression of ITGB4. TCN1-knockdown promoted the degradation of ITGB4 and increased the instability of ITGB4 and filamin A (FLNA). Downregulation of ITGB4 at the protein level resulted in the disassociation of the ITGB4/PLEC complex, leading to cytoskeletal damage. Conclusion: TCN1 might exert oncogenic role in CRC via regulating the ITGB4 signaling pathway.

scholarly journals Long noncoding RNA GAS5 inhibits progression of colorectal cancer by interacting with and triggering YAP phosphorylation and degradation and is negatively regulated by the m6A reader YTHDF3

2019 ◽  
Vol 18 (1) ◽  
Author(s):  
Wen Ni ◽  
Su Yao ◽  
Yunxia Zhou ◽  
Yuanyuan Liu ◽  
Piao Huang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Cancer Progression ◽  
Noncoding Rna ◽  
Function Analysis ◽  
Loss Of Function ◽  
Functional Link ◽  
Protein Levels ◽  
Lncrna Gas5

Abstract Background YAP activation is crucial for cancer development including colorectal cancer (CRC). Nevertheless, it remains unclear whether N6-Methyladenosine (m6A) modified transcripts of long noncoding RNAs (lncRNAs) can regulate YAP activation in cancer progression. We investigated the functional link between lncRNAs and the m6A modification in YAP signaling and CRC progression. Methods YAP interacting lncRNAs were screened by RIP-sequencing, RNA FISH and immunofluorescence co-staining assays. Interaction between YAP and lncRNA GAS5 was studied by biochemical methods. MeRIP-sequencing combined with lncRNA-sequencing were used to identify the m6A modified targets of YTHDF3 in CRC. Gain-of-function and Loss-of-function analysis were performed to measure the function of GAS5-YAP-YTHDF3 axis in CRC progression in vitro and in vivo. Results GAS5 directly interacts with WW domain of YAP to facilitate translocation of endogenous YAP from the nucleus to the cytoplasm and promotes phosphorylation and subsequently ubiquitin-mediated degradation of YAP to inhibit CRC progression in vitro and in vivo. Notably, we demonstrate the m6A reader YTHDF3 not only a novel target of YAP but also a key player in YAP signaling by facilitating m6A-modified lncRNA GAS5 degradation, which profile a new insight into CRC progression. Clinically, lncRNA GAS5 expressions is negatively correlated with YAP and YTHDF3 protein levels in tumors from CRC patients. Conclusions Our study uncovers a negative functional loop of lncRNA GAS5-YAP-YTHDF3 axis, and identifies a new mechanism for m6A-induced decay of GAS5 on YAP signaling in progression of CRC which may offer a promising approach for CRC treatment.

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