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1
Jochumsen, Nicholas, Yang Liu, Søren Molin, and Anders Folkesson. "A Mig-14-like protein (PA5003) affects antimicrobial peptide recognition in Pseudomonas aeruginosa." Microbiology 157, no. 9 (September 1, 2011): 2647–57. http://dx.doi.org/10.1099/mic.0.049445-0.
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The evolution of antibiotic resistance in pathogenic bacteria is a growing global health problem which is gradually making the treatment of infectious diseases less efficient. Antimicrobial peptides are small charged molecules found in organisms from the complete phylogenetic spectrum. The peptides are attractive candidates for novel drug development due to their activity against bacteria that are resistant to conventional antibiotics, and reports of peptide resistance are rare in the clinical setting. Paradoxically, many clinically relevant bacteria have mechanisms that can recognize and respond to the presence of cationic antimicrobial peptides (CAMPs) in the environment by changing the properties of the microbial surface thereby increasing the tolerance of the microbes towards the peptides. In Pseudomonas aeruginosa an essential component of this inducible tolerance mechanism is the lipopolysaccharide modification operon arnBCADTEF–PA3559 which encodes enzymes required for LPS alterations leading to increased antimicrobial peptide tolerance. The expression of the operon is induced by the presence of CAMPs in the environment but the molecular mechanisms underlying the cellular recognition of the peptides are poorly elucidated. In this work, we investigate the factors influencing arnB expression by transposon mutagenesis and arnB promoter green fluorescent protein reporters. We have identified a novel gene encoding a Mig-14-like protein that is required for recognition of the CAMPs colistin and Novispirin G10 by P. aeruginosa. Moreover, we show that this gene is also required for the formation of CAMP-tolerant subpopulations in P. aeruginosa hydrodynamic flow chamber biofilms.
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White, David T., Katie M. McShea, Myriam A. Attar, and Lorraine C. Santy. "GRASP and IPCEF Promote ARF-to-Rac Signaling and Cell Migration by Coordinating the Association of ARNO/cytohesin 2 with Dock180." Molecular Biology of the Cell 21, no. 4 (February 15, 2010): 562–71. http://dx.doi.org/10.1091/mbc.e09-03-0217.
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ARFs are small GTPases that regulate vesicular trafficking, cell shape, and movement. ARFs are subject to extensive regulation by a large number of accessory proteins. The many different accessory proteins are likely specialized to regulate ARF signaling during particular processes. ARNO/cytohesin 2 is an ARF-activating protein that promotes cell migration and cell shape changes. We report here that protein–protein interactions mediated by the coiled-coil domain of ARNO are required for ARNO induced motility. ARNO lacking the coiled-coil domain does not promote migration and does not induce ARF-dependent Rac activation. We find that the coiled-coil domain promotes the assembly of a multiprotein complex containing both ARNO and the Rac-activating protein Dock180. Knockdown of either GRASP/Tamalin or IPCEF, two proteins known to bind to the coiled-coil of ARNO, prevents the association of ARNO and Dock180 and prevents ARNO-induced Rac activation. These data suggest that scaffold proteins can regulate ARF dependent processes by biasing ARF signaling toward particular outputs.
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Xu, Xingjian, Igor Dikiy, Matthew R. Evans, Leandro P. Marcelino, and Kevin H. Gardner. "Fragile protein folds: sequence and environmental factors affecting the equilibrium of two interconverting, stably folded protein conformations." Magnetic Resonance 2, no. 1 (March 10, 2021): 63–76. http://dx.doi.org/10.5194/mr-2-63-2021.
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Abstract. Recent research on fold-switching metamorphic proteins has revealed some notable exceptions to Anfinsen's hypothesis of protein folding. We have previously described how a single point mutation can enable a well-folded protein domain, one of the two PAS (Per-ARNT-Sim) domains of the human ARNT (aryl hydrocarbon receptor nuclear translocator) protein, to interconvert between two conformers related by a slip of an internal β strand. Using this protein as a test case, we advance the concept of a “fragile fold”, a protein fold that can reversibly rearrange into another fold that differs by a substantial number of hydrogen bonds, entailing reorganization of single secondary structure elements to more drastic changes seen in metamorphic proteins. Here we use a battery of biophysical tests to examine several factors affecting the equilibrium between the two conformations of the switching ARNT PAS-B Y456T protein. Of note is that we find that factors which impact the HI loop preceding the shifted Iβ strand affect both the equilibrium levels of the two conformers and the denatured state which links them in the interconversion process. Finally, we describe small molecules that selectively bind to and stabilize the wild-type conformation of ARNT PAS-B. These studies form a toolkit for studying fragile protein folds and could enable ways to modulate the biological functions of such fragile folds, both in natural and engineered proteins.
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Lee, Soo Chan, Sabrina N. Schmidtke, Lawrence J. Dangott, and Brian D. Shaw. "Aspergillus nidulans ArfB Plays a Role in Endocytosis and Polarized Growth." Eukaryotic Cell 7, no. 8 (June 6, 2008): 1278–88. http://dx.doi.org/10.1128/ec.00039-08.
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ABSTRACT Filamentous fungi undergo polarized growth throughout most of their life cycles. The Spitzenkörper is an apical organelle composed primarily of vesicles that is unique to filamentous fungi and is likely to act as a vesicle supply center for tip growth. Vesicle assembly and trafficking are therefore important for hyphal growth. ADP ribosylation factors (Arfs), a group of small GTPase proteins, play an important role in nucleating vesicle assembly. Little is known about the role of Arfs in filamentous hyphal growth. We found that Aspergillus nidulans is predicted to encode six Arf family proteins. Analysis of protein sequence alignments suggests that A. nidulans ArfB shares similarity with ARF6 of Homo sapiens and Arf3p of Saccharomyces cerevisiae. An arfB null allele (arfB disrupted by a transposon [arfB::Tn]) was characterized by extended isotropic growth of germinating conidia followed by cell lysis or multiple, random germ tube emergence, consistent with a failure to establish polarity. The mutant germ tubes and hyphae that do form initially meander abnormally off of the axis of polarity and frequently exhibit dichotomous branching at cell apices, consistent with a defect in polarity maintenance. FM4-64 staining of the arfB::Tn strain revealed that another phenotypic characteristic seen for arfB::Tn is a reduction and delay in endocytosis. ArfB is myristoylated at its N terminus. Green fluorescent protein-tagged ArfB (ArfB::GFP) localizes to the plasma membrane and endomembranes and mutation (ArfBG2A::GFP) of the N-terminal myristoylation motif disperses the protein to the cytoplasm rather than to the membranes. These results demonstrate that ArfB functions in endocytosis to play important roles in polarity establishment during isotropic growth and polarity maintenance during hyphal extension.
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Aitola, Marjo, Christine M. Sadek, Jan-Åke Gustafsson, and Markku Pelto-Huikko. "Aint/Tacc3 Is Highly Expressed in Proliferating Mouse Tissues During Development, Spermatogenesis, and Oogenesis." Journal of Histochemistry & Cytochemistry 51, no. 4 (April 2003): 455–69. http://dx.doi.org/10.1177/002215540305100407.
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Aint was originally identified on the basis of its interaction in vitro with the aryl hydrocarbon nuclear receptor translocator (Arnt). Arnt is a common heterodimerization partner in the basic helix-loop–helix (bHLH)-PER-ARNT-SIM (PAS) protein family and is involved in diverse biological functions. These include xenobiotic metabolism, hypoxic response, and circadian rhythm. In addition, Arnt has a crucial role during development. Aint is a member of a growing family of transforming acidic coiled-coil (TACC) proteins and is the murine homologue of human TACC3. Here we report the spatiotemporal expression of Tacc3 mRNA and protein in embryonic, postnatally developing, and adult mouse tissues using in situ hybridization and immunocytochemistry. Tacc3 mRNA was highly expressed in proliferating cells of several organs during murine development. However, the only adult tissues expressing high levels were testis and ovary. Immunocytochemistry revealed that Tacc3 is a nuclear protein. Our results suggest that Tacc3 has an important role in murine development, spermatogenesis, and oogenesis.
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Reimann, Julia, Kerstin Lassak, Sunia Khadouma, Thijs J. G. Ettema, Nuan Yang, Arnold J. M. Driessen, Andreas Klingl, and Sonja-Verena Albers. "Regulation of archaella expression by the FHA and von Willebrand domain-containing proteins ArnA and ArnB inSulfolobus acidocaldarius." Molecular Microbiology 86, no. 1 (August 22, 2012): 24–36. http://dx.doi.org/10.1111/j.1365-2958.2012.08186.x.
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Moffett, P., M. Reece, and J. Pelletier. "The murine Sim-2 gene product inhibits transcription by active repression and functional interference." Molecular and Cellular Biology 17, no. 9 (September 1997): 4933–47. http://dx.doi.org/10.1128/mcb.17.9.4933.
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The Drosophila single-minded (Dsim) gene encodes a master regulatory protein involved in cell fate determination during midline development. This protein is a member of a rapidly expanding family of gene products possessing basic helix-loop-helix (bHLH) and hydrophobic PAS (designated a conserved region among PER, ARNT [aryl hydrocarbon receptor nuclear translocator] and SIM) protein association domains. Members of this family function as central transcriptional regulators in cellular differentiation and in the response to environmental stimuli such as xenobiotics and hypoxia. We have previously identified a murine member of this family, called mSim-2, showing sequence homology to the bHLH and PAS domains of Dsim. Immunoprecipitation experiments with recombinant proteins indicate that mSIM-2 associates with the arnt gene product. In the present work, by using fine-structure mapping we found that the HLH and PAS motifs of both proteins are required for optimal association. Forced expression of GAL4/mSIM-2 fusion constructs in mammalian cells demonstrated the presence of two separable repression domains within the carboxy terminus of mSIM-2. We found that mSIM-2 is capable of repressing ARNT-mediated transcriptional activation in a mammalian two-hybrid system. This effect (i) is dependent on the ability of mSIM-2 and ARNT to heterodimerize, (ii) is dependent on the presence of the mSIM-2 carboxy-terminal repression domain, and (iii) is not specific to the ARNT activation domain. These results suggest that mSIM-2 repression activity can dominantly override the activation potential of adjacent transcription factors. We also demonstrated that mSIM-2 can functionally interfere with hypoxia-inducible factor 1alpha (HIF-1alpha)/ARNT transcription complexes, providing a second mechanism by which mSIM-2 may inhibit transcription.
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Wang, Feng, Shengli Shi, Ruixue Zhang, and Oliver Hankinson. "Identifying target genes of the aryl hydrocarbon receptor nuclear translocator (Arnt) using DNA microarray analysis." Biological Chemistry 387, no. 9 (September 1, 2006): 1215–18. http://dx.doi.org/10.1515/bc.2006.150.
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Abstract The aryl hydrocarbon receptor nuclear translocator (Arnt) is a basic helix-loop-helix (bHLH) protein that also contains a Per-Arnt-Sim (PAS) domain. In addition to forming heterodimers with many other bHLH-PAS proteins, including the aryl hydrocarbon receptor (AhR) and hypoxia-inducible factors 1α, 2α and 3α, Arnt can also form homodimers when expressed from its cDNA in vitro or in vivo. However, target genes of the Arnt/Arnt homodimer remain to be identified. In this study, we have elucidated the profile of genes responsive to the reintroduction of Arnt expression in an Arnt-deficient mouse hepatoma cell line (c4), using DNA microarray analysis. The expression of 27 genes was upregulated by 1.5-fold or more in c4 cells infected with a retroviral vector expressing mouse Arnt, while no genes were found to be downregulated. Among the upregulated genes, BCL2/adenovirus E1B 19 kDa-interacting protein 1 (NIP3), serine (or cysteine) proteinase inhibitor, clade E, member 1 (PAI1), and N-myc downstream regulated-like (NDR1), were confirmed to be induced by Arnt using real-time PCR. We also found that the 5′ promoter region of 15 out of 20 upregulated genes contain the type 2 E-box 5′-CACGTG-3′ Arnt/Arnt binding sequence, consistent with the notion that they represent target genes for Arnt.
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Hoffmann, Lena, Andreas Schummer, Julia Reimann, Maria F. Haurat, Amanda J. Wilson, Morgan Beeby, Bettina Warscheid, and Sonja-V. Albers. "Expanding the archaellum regulatory network - the eukaryotic protein kinases ArnC and ArnD influence motility ofSulfolobus acidocaldarius." MicrobiologyOpen 6, no. 1 (October 22, 2016): e00414. http://dx.doi.org/10.1002/mbo3.414.
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Coban, Mathew A., Patrick R. Blackburn, Murray L. Whitelaw, Mieke M. van Haelst, Paldeep S. Atwal, and Thomas R. Caulfield. "Structural Models for the Dynamic Effects of Loss-of-Function Variants in the Human SIM1 Protein Transcriptional Activation Domain." Biomolecules 10, no. 9 (September 12, 2020): 1314. http://dx.doi.org/10.3390/biom10091314.
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Single-minded homologue 1 (SIM1) is a transcription factor with numerous different physiological and developmental functions. SIM1 is a member of the class I basic helix-loop-helix-PER-ARNT-SIM (bHLH–PAS) transcription factor family, that includes several other conserved proteins, including the hypoxia-inducible factors, aryl hydrocarbon receptor, neuronal PAS proteins, and the CLOCK circadian regulator. Recent studies of HIF-a-ARNT and CLOCK-BMAL1 protein complexes have revealed the organization of their bHLH, PASA, and PASB domains and provided insight into how these heterodimeric protein complexes form; however, experimental structures for SIM1 have been lacking. Here, we describe the first full-length atomic structural model for human SIM1 with its binding partner ARNT in a heterodimeric complex and analyze several pathogenic variants utilizing state-of-the-art simulations and algorithms. Using local and global positional deviation metrics, deductions to the structural basis for the individual mutants are addressed in terms of the deleterious structural reorganizations that could alter protein function. We propose new experiments to probe these hypotheses and examine an interesting SIM1 dynamic behavior. The conformational dynamics demonstrates conformational changes on local and global regions that represent a mechanism for dysfunction in variants presented. In addition, we used our ab initio hybrid model for further prediction of variant hotspots that can be engineered to test for counter variant (restoration of wild-type function) or basic research probe.
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Bischof, Lisa Franziska, Maria Florencia Haurat, and Sonja-Verena Albers. "Two membrane-bound transcription factors regulate expression of various type-IV-pili surface structures in Sulfolobus acidocaldarius." PeerJ 7 (February 26, 2019): e6459. http://dx.doi.org/10.7717/peerj.6459.
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In Archaea and Bacteria, gene expression is tightly regulated in response to environmental stimuli. In the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius nutrient limitation induces expression of the archaellum, the archaeal motility structure. This expression is orchestrated by a complex hierarchical network of positive and negative regulators—the archaellum regulatory network (arn). The membrane-bound one-component system ArnR and its paralog ArnR1 were recently described as main activators of archaellum expression in S. acidocaldarius. They regulate gene expression of the archaellum operon by targeting the promoter of flaB, encoding the archaellum filament protein. Here we describe a strategy for the isolation and biochemical characterization of these two archaellum regulators. Both regulators are capable of forming oligomers and are phosphorylated by the Ser/Thr kinase ArnC. Apart from binding to pflaB, ArnR but not ArnR1 bound to promoter sequences of aapF and upsX, which encode components of the archaeal adhesive pilus and UV-inducible pili system, demonstrating a regulatory connection between different surface appendages of S. acidocaldarius.
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HULKKO, Sanna M., Hideki WAKUI, and Johanna ZILLIACUS. "The pro-apoptotic protein death-associated protein 3 (DAP3) interacts with the glucocorticoid receptor and affects the receptor function." Biochemical Journal 349, no. 3 (July 25, 2000): 885–93. http://dx.doi.org/10.1042/bj3490885.
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The yeast two-hybrid system was used to isolate cDNAs encoding proteins that interact with the glucocorticoid receptor (GR) ligand-binding domain in a ligand-dependent manner. One isolated cDNA encoded a fragment of death-associated protein 3 (DAP3), which has been implicated as a positive mediator of apoptosis. In vitro experiments showed that the full-length DAP3 also interacted with GR. The main interaction domain was mapped to the N-terminal region of DAP3 that had previously been shown to function in a dominant-negative fashion, protecting cells from apoptosis. Co-transfection experiments in COS-7 cells showed that DAP3 had a stimulatory effect on the ligand-induced transcriptional activation by GR and also increased the steroid-sensitivity. Furthermore, DAP3 formed a complex with several other nuclear receptors and some basic helix–loop–helix/Per–Arnt–Sim proteins, as well as with heat-shock protein 90 (hsp90) (Arnt is the aryl-hydrocarbon-receptor nuclear translocator, and Per and Sim are the Drosophila proteins Period and Single-minded). The results suggest that DAP3 could have an important role in GR action, possibly by modulating the cytoplasmic GR–hsp90 complex. Since glucocorticoids can induce apoptosis, the pro-apoptotic DAP3 protein may be involved in this function of GR.
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Georgellis, Dimitris, Ohsuk Kwon, Edmund C. C. Lin, Sandy M. Wong, and Brian J. Akerley. "Redox Signal Transduction by the ArcB Sensor Kinase of Haemophilus influenzae Lacking the PAS Domain." Journal of Bacteriology 183, no. 24 (December 15, 2001): 7206–12. http://dx.doi.org/10.1128/jb.183.24.7206-7212.2001.
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ABSTRACT The Arc (anoxic redox control) two-component signal transduction system of Escherichia coli, which comprises the tripartite ArcB sensor kinase and the ArcA response regulator, modulates the expression of numerous operons in response to redox conditions of growth. We demonstrate that the arcA and arcBgenes of Haemophilus influenzae specify a two-component system. The Arc proteins of the two bacterial species sufficiently resemble each other that they can participate in heterologous transphosphorylation in vitro. Moreover, the Arc system of H. influenzae mediates transcriptional control according to the redox condition of growth both autologously in its own host and homologously in E. coli, indicating a high degree of functional conservation of the signal transduction system. The H. influenzae ArcB, however, lacks the PAS domain present in the region of E. coli ArcB linking the transmembrane to the cytosolic catalytic domains. Because the PAS domain participates in signal reception in a variety of sensory proteins, including sensors of molecular oxygen and redox state, a similar role was previously ascribed to it in ArcB. Our results demonstrate that the ArcB protein of H. influenzae mediates signal transduction in response to redox conditions of growth despite the absence of the PAS domain.
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Wang, Xinyue, Jingjing Bao, Yazhen Bi, Wenping Hu, and Li Zhang. "Polymorphism, Expression, and Structure Analysis of a Key Gene ARNT in Sheep (Ovis aries)." Biology 11, no. 12 (December 10, 2022): 1795. http://dx.doi.org/10.3390/biology11121795.
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Growth traits are influential factors that significantly affects the development of the sheep industry. A previous TMT proteomic analysis found that a key protein in the HIF signaling pathway, ARNT, may influence embryonic skeletal muscle growth and development in sheep. The purpose of this study was to better understand the association between the polymorphisms of ARNT and growth traits of sheep, and the potential function of ARNT. Real-time qPCR (qRT-PCR) of ARNT was carried out to compare its expression in different developmental stages of the muscle tissues and primary myoblasts in the Hu, Chinese merino, and Gangba sheep. The genetic variance of ARNT was detected using the Illumina Ovine SNP 50 K and 600 K BeadChip in the Hu and Ujimqin sheep populations, respectively. The CDS sequence of the ARNT gene was cloned in the Hu sheep using PCR technology. Finally, bioinformatic analytical methods were applied to characterize the genes and their hypothetical protein products. The qRT-PCR results showed that the ARNT gene was expressed significantly in the Chinese merino embryo after 85 gestation days (D85) (p < 0.05). Additionally, after the sheep were born, the expression of ARNT was significant at the weaning stage of the Hu sheep (p < 0.01). However, there was no difference in the Gangba sheep.In addition, six SNP loci were screened using 50 K and 600 K BeadChip. We found a significant association between rs413597480 A > G and the Hu sheep weight at weaning and backfat thickness in the 5-month-old sheep (p < 0.05), and four SNP loci (rs162298018 G > C, rs159644025 G > A, rs421351865 G > A, and rs401758103 A > G) were also associated with growth traits in the Ujimqin sheep (p < 0.05). Interestingly, we found that a G > C mutation at 1948 bp in the cloned ARNT CDS sequence of the Hu sheep was the same locus mutation as rs162298018 G > C identified using the 600 K BeadChip, which resulted in a nonconservative missense point mutation, leading to a change from proline to alanine and altering the number of DNA, protein-binding sites, and the α-helix of the ARNT protein. There was a strong linkage disequilibrium between rs162298018 G > C and rs159644025 G > A, and the ARNT protein was conserved among the goat, Hu sheep, and Texel sheep. And, we propose that a putative molecular marker for growth and development in sheep may be the G > C mutation at 1948 bp in the CDS region of the ARNT gene. Our study systematically analyzed the expression, structure, and function of the ARNT gene and its encoded proteins in sheep. This provides a basis for future studies of the regulatory mechanisms of the ARNT gene.
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Brown, Roslyn N., James A. Sanford, Jea H. Park, Brooke L. Deatherage, Boyd L. Champion, Richard D. Smith, Fred Heffron, and Joshua N. Adkins. "A Comprehensive Subcellular Proteomic Survey of Salmonella Grown under Phagosome-Mimicking versus Standard Laboratory Conditions." International Journal of Proteomics 2012 (July 25, 2012): 1–12. http://dx.doi.org/10.1155/2012/123076.
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Towards developing a systems-level pathobiological understanding of Salmonella enterica, we performed a subcellular proteomic analysis of this pathogen grown under standard laboratory and phagosome-mimicking conditions in vitro. Analysis of proteins from cytoplasmic, inner membrane, periplasmic, and outer membrane fractions yielded coverage of 25% of the theoretical proteome. Confident subcellular location could be assigned to over 1000 proteins, with good agreement between experimentally observed location and predicted/known protein properties. Comparison of protein location under the different environmental conditions provided insight into dynamic protein localization and possible moonlighting (multiple function) activities. Notable examples of dynamic localization were the response regulators of two-component regulatory systems (e.g., ArcB and PhoQ). The DNA-binding protein Dps that is generally regarded as cytoplasmic was significantly enriched in the outer membrane for all growth conditions examined, suggestive of moonlighting activities. These observations imply the existence of unknown transport mechanisms and novel functions for a subset of Salmonella proteins. Overall, this work provides a catalog of experimentally verified subcellular protein locations for Salmonella and a framework for further investigations using computational modeling.
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Zimmermann, Rainer, Volkhard A. J. Kempf, Emile Schiltz, Karin Oberle, and Anna Sander. "Hemin Binding, Functional Expression, and Complementation Analysis of Pap 31 from Bartonella henselae." Journal of Bacteriology 185, no. 5 (March 1, 2003): 1739–44. http://dx.doi.org/10.1128/jb.185.5.1739-1744.2003.
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ABSTRACT Growth of Bartonella henselae is strongly heme dependent, and B. henselae is unable to synthesize heme itself. At least five outer membrane-associated proteins from B. henselae bind hemin, including the 31-kDa protein designated Pap31. The gene of this protein was heterologously expressed in Escherichia coli M15(pREP4) and detected with monoclonal antibodies in the outer membrane fraction. Complementation of the hemA-deficient mutant E. coli K-12 EB53 (aroB tsx malT hemA) with pap31 demonstrated that this protein is involved in heme acquisition and may be an important virulence factor in the pathogenesis of B. henselae.
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Monier, S., P. Chardin, S. Robineau, and B. Goud. "Overexpression of the ARF1 exchange factor ARNO inhibits the early secretory pathway and causes the disassembly of the Golgi complex." Journal of Cell Science 111, no. 22 (November 15, 1998): 3427–36. http://dx.doi.org/10.1242/jcs.111.22.3427.
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The small GTPase ARF1 is a key regulator of intracellular membrane traffic. In its active, GTP-bound form, ARF1 is associated with Golgi membranes and promotes the recruitment of the cytosolic coat protein complex, which will result in membrane budding and vesicle formation. ARNO (ARF nucleotide site opener) has been shown to act in vitro as a GTP exchange factor for ARF1. Here, we have investigated the function of ARNO in vivo. By immunofluorescence and cell fractionation, ARNO was found to be mostly cytosolic in HeLa cells. Its overexpression led to a strong inhibition of the secretion of SEAP (secreted form of alkaline phosphatase). Newly synthesized SEAP failed to acquire endoglycosidase H resistance, indicating a block in the early secretory pathway. This effect on secretion was accompanied by a disassembly of the Golgi complex and a redistribution of Golgi resident proteins into the endoplasmic reticulum (ER). On the other hand, ARNO overexpression did not affect the early endocytic pathway. These results show that ARNO functions in vivo in Golgi to ER transport. Its behavior is then consistent with ARNO being an exchange factor for ARF1.
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Herni, Laily Agustina, and A. Mujnisa. "Herni Pengaruh Imbangan Energi-Protein Terhadap Bobot dan Tebal Kerabang Telur Ayam Arab." Jurnal Sains dan Teknologi Peternakan 3, no. 2 (June 28, 2022): 55–59. http://dx.doi.org/10.31605/jstp.v3i2.1686.
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Penelitian bertujuan mengetahui imbangan protein dan energi yang paling tepat dalam menghasilkan bobot dan ketebalan kerabang telur ayam Arab. Komposisi ransum terdiri dari: jagung kuning, dedak, dan konsentrat RK 24 yang disusun berdasarkan imbangan energi dan protein. Penelitian ini menggunakan Rancangan Acak Lengkap (RAL) terdiri dari 4 perlakuan dan 10 ulangan terdiri dari 40 petak percobaan degan masing-masing petak terdiri dari 2 ekor ayam, sehingga total ayam Arab yang digunakan sebanyak 80 ekor. Perlakuan terdiri dari: R1 (protein 15 % dengan energi metabolisme 2500 kkal/kg); R2 (protein 16 % dengan energi metabolisme 2600 kkal/kg); R3 (protein 17 % dengan energi metabolisme 2700 kkal/kg); dan R4 (protein 18 % dengan energi metabolisme 2800 kkal/kg). Hasil penelitian menunjukkan bahwa imbangan energi dan protein tidak berpengaruh nyata (P>0,05) terhadap bobot dan tebal kerabang telur ayam Arab. Rataan bobot telur yang dihasilkan berkisar antara 37,24 – 39,15 g sedangkan rataan tebal kerabang yang dihasilkan berkisar antara 0,42 – 0,46 mm terhadap telur ayam Arab umur 5 bulan. Disimpulkan bahwa pemberian ransum dengan level protein 18 % dan energi 2800 kkal meningkatkan bobot telur dan tebal kerabang ayam Arab petelur.
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Adaixo, Ricardo, and João Henrique Morais-Cabral. "Crystallization and preliminary crystallographic characterization of the PAS domains of EAG and ELK potassium channels." Acta Crystallographica Section F Structural Biology and Crystallization Communications 66, no. 9 (August 26, 2010): 1056–59. http://dx.doi.org/10.1107/s1744309110027880.
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Per–Arnt–Sim (PAS) domains are ubiquitous in nature; they are ∼130-amino-acid protein domains that adopt a fairly conserved three-dimensional structure despite their low degree of sequence homology. These domains constitute the N-terminus or, less frequently, the C-terminus of a number of proteins, where they exert regulatory functions. PAS-containing proteins generally display two or more copies of this motif. In this work, the crystallization and preliminary analysis of the PAS domains of two eukaryotic potassium channels from the ether-à-go-go (EAG) family are reported.
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Purdel, Nicoleta. "Current Methods Used in the Protein Carbonyl Assay." Annual Research & Review in Biology 4, no. 12 (January 10, 2014): 2015–26. http://dx.doi.org/10.9734/arrb/2014/8763.
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Liu, Xiaojing, Renwu Cheng, Yu Chen, Shengkun Wang, Fangcuo Qin, Dongli Wang, Yunshan Liu, Lipan Hu, and Sen Meng. "Identification and Characterization of the AREB/ABF/ABI5 Gene Family in Sandalwood (Santalum album L.) and Its Potential Role in Drought Stress and ABA Treatment." Forests 14, no. 8 (August 21, 2023): 1691. http://dx.doi.org/10.3390/f14081691.
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AREB/ABF/ABI5 (ABA-responsive element-binding protein/ABRE binding factors and ABA INSENSITIVE 5) transcription factors are involved in regulating the expression of ABA (abscisic acid)-related genes and improving plant adaptability to environmental stress. To explore the influence of AREB/ABF transcription factors on santalol synthesis, we conducted a genome-wide analysis of the AREB gene family in sandalwood, identified 10 SaAREB genes, and divided them into five subfamilies. We found that all SaAREB genes encoded unstable hydrophilic proteins and the subcellular localization prediction of SaAREBs was that they are located in the nucleus. AREB/ABF genes belong to the bZIP-A subfamily and we found that the 10 AREB proteins all contained bZIP (basic region leucine zipper) and four potential phosphorylation sites (RXXS/T). According to the collinearity analysis results, four of the SaAREB genes were involved in two fragment duplication events. Through qRT-PCR (real-time fluorescence quantitative PCR), we explored the expression profile of SaAREB in different tissues; the effects of ABA treatment and drought treatment on AREB transcription factors were predicted. From the expression of different tissues, we found that SaAREB1 not only responded to prolonged drought but also was highly expressed in stems. Moreover, SaAREB3, SaAREB7, and SaAREB8 specifically respond to ABA treatment. Based on RNA-seq (RNA sequencing) data, we found that SaAREB6 and SaAREB8 were highly expressed in the sapwood and transition regions. Regarding SaCYP736A167, as a key gene in santalol synthesis, its promoter contains the most ABRE cis-reactive elements. These results provide a basis for further analysis of the role of the Santalum album L. (S. album) ABRE/ABF/ABI5 genes in the formation of santalols.
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Lee, S. Y., and B. Pohajdak. "N-terminal targeting of guanine nucleotide exchange factors (GEF) for ADP ribosylation factors (ARF) to the Golgi." Journal of Cell Science 113, no. 11 (June 1, 2000): 1883–89. http://dx.doi.org/10.1242/jcs.113.11.1883.
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B2-1 (cytohesin-1) is a member of a group of proteins (including ARNO and ARNO3) that are all of similar size and domain composition. The three proteins contain an N-terminal coiled-coil domain, followed by a Sec7 and a pleckstrin homology (PH) domain. While it is well established that the Sec7 domain functions as a guanine nucleotide exchange factor (GEF) for ADP-ribosylation factors (ARFs) and the PH domain anchors the proteins to membrane phosphoinositols, the function of the N-terminal domain is unknown. Here we show that the N terminus of B2-1 (residues 1–54) is necessary and sufficient to target the protein to the Golgi. The Sec7+PH domains of B2-1 (residues 55–398) are not sufficient for Golgi localization. Further deletion analysis and point mutagenesis indicate that the coiled-coil domain within the N terminus is responsible for Golgi targeting. Furthermore, ARNO and ARNO3 N termini also have the same capability of targeting to the Golgi. We conclude that the N-terminal, (α)-helical, coiled-coil domain is used to target this family of proteins to the Golgi complex.
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Merkulova, Maria, Andrés Hurtado-Lorenzo, Hiroyuki Hosokawa, Zhenjie Zhuang, Dennis Brown, Dennis A. Ausiello, and Vladimir Marshansky. "Aldolase directly interacts with ARNO and modulates cell morphology and acidic vesicle distribution." American Journal of Physiology-Cell Physiology 300, no. 6 (June 2011): C1442—C1455. http://dx.doi.org/10.1152/ajpcell.00076.2010.
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Previously, we demonstrated that the vacuolar-type H+-ATPase (V-ATPase) a2-subunit functions as an endosomal pH sensor that interacts with the ADP-ribosylation factor (Arf) guanine nucleotide exchange factor, ARNO. In the present study, we showed that ARNO directly interacts not only with the a2-subunit but with all a-isoforms (a1–a4) of the V-ATPase, indicating a widespread regulatory interaction between V-ATPase and Arf GTPases. We then extended our search for other ARNO effectors that may modulate V-ATPase-dependent vesicular trafficking events and actin cytoskeleton remodeling. Pull-down experiments using cytosol of mouse proximal tubule cells (MTCs) showed that ARNO interacts with aldolase, but not with other enzymes of the glycolytic pathway. Direct interaction of aldolase with the pleckstrin homology domain of ARNO was revealed by pull-down assays using recombinant proteins, and surface plasmon resonance revealed their high avidity interaction with a dissociation constant: KD = 2.84 × 10−10 M. MTC cell fractionation revealed that aldolase is also associated with membranes of early endosomes. Functionally, aldolase knockdown in HeLa cells produced striking morphological changes accompanied by long filamentous cell protrusions and acidic vesicle redistribution. However, the 50% knockdown we achieved did not modulate the acidification capacity of endosomal/lysosomal compartments. Finally, a combination of small interfering RNA knockdown and overexpression revealed that the expression of aldolase is inversely correlated with gelsolin levels in HeLa cells. In summary, we have shown that aldolase forms a complex with ARNO/Arf6 and the V-ATPase and that it may contribute to remodeling of the actin cytoskeleton and/or the trafficking and redistribution of V-ATPase-dependent acidic compartments via a combination of protein-protein interaction and gene expression mechanisms.
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Kishore, V., and H. Puttaraju. "Molecular Dynamics, Simulation of Protein-Protein Complex and their Role in Cytoprotective Process in Ethanol-induced Toxicity of HepG2 Cell Line." Annual Research & Review in Biology 27, no. 6 (August 4, 2018): 1–9. http://dx.doi.org/10.9734/arrb/2018/43227.
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Brody, Stuart. "A Comparison of the Neurospora and Drosophila Clocks." Journal of Biological Rhythms 35, no. 2 (December 26, 2019): 119–33. http://dx.doi.org/10.1177/0748730419892434.
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In Neurospora and other fungi, the protein frequency (FRQ) is an integral part and a negative element in the fungal circadian oscillator. In Drosophila and many other higher organisms, the protein period (PER) is an integral part and a negative element of their circadian oscillator. Employing bioinformatic techniques, such as BLAST, CLUSTAL, and MEME (Multiple Em for Motif Elicitation), 11 regions (sequences) of potential similarity were found between the fungal FRQ and the Drosophila PER. Many of these FRQ regions are conserved in many fungal FRQ(s). Many of these PER regions are conserved in many insects. In addition, these regions are also of biological significance since mutations in these regions lead to changes in the circadian clock of Neurospora and Drosophila. Many of these regions of similarity between FRQ and PER are also conserved between the Drosophila PER and the mouse PER (mPER2). This suggests conserved and important regions for all 3 proteins and a common ancestor, possibly in those amoeba, such as Capsaspora, that sits at the base of the phylogenetic tree where fungi and animals diverged. Two additional examples of a possible common ancestor between Neurospora and Drosophila were found. One, the white collar (WC-1) protein of Neurospora and the Drosophila PER, shows significant similarity in its Per/Arnt/Sim (PAS) motifs to the PAS motif of an ARNT-like protein found in the amoeba, Capsaspora. Two, both of the positive elements in each system (i.e., WC-1 in Neurospora and cycle [CYC] in Drosophila), show significant similarity to this Capsaspora ARNT protein. A discussion of these findings centers on the long-time debate about the origins of the many different clock systems (i.e., independent evolution or common ancestor as well as to the question of how new genes are formed).
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Kudryavtseva, A. A., I. S. Okhrimenko, V. S. Didina, G. B. Zavilgelsky, and I. V. Manukhov. "Antirestriction Protein ArdB (R64) Interacts with DNA." Biochemistry (Moscow) 85, no. 3 (March 2020): 318–25. http://dx.doi.org/10.1134/s0006297920030074.
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Kopp, Ulla C., Donna M. Farley, Michael Z. Cicha, and Lori A. Smith. "Activation of renal mechanosensitive neurons involves bradykinin, protein kinase C, PGE2, and substance P." American Journal of Physiology-Regulatory, Integrative and Comparative Physiology 278, no. 4 (April 1, 2000): R937—R946. http://dx.doi.org/10.1152/ajpregu.2000.278.4.r937.
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Increased renal pelvic pressure or bradykinin increases afferent renal nerve activity (ARNA) via PGE2-induced release of substance P. Protein kinase C (PKC) activation increases ARNA, and PKC inhibition blocks the ARNA response to bradykinin. We now examined whether bradykinin mediates the ARNA response to increased renal pelvic pressure by activating PKC. In anesthetized rats, the ARNA responses to increased renal pelvic pressure were blocked by renal pelvic perfusion with the bradykinin B2-receptor antagonist HOE 140 and the PKC inhibitor calphostin C by 76 ± 8% ( P < 0.02) and 81 ± 5% ( P < 0.01), respectively. Renal pelvic perfusion with 4β-phorbol 12,13-dibutyrate (PDBu) to activate PKC increased ARNA 27 ± 4% and renal pelvic release of PGE2 from 500 ± 59 to 1,113 ± 183 pg/min and substance P from 10 ± 2 to 30 ± 2 pg/min (all P < 0.01). Indomethacin abolished the increases in substance P release and ARNA. The PDBu-mediated increase in ARNA was also abolished by the substance P-receptor antagonist RP 67580. We conclude that bradykinin contributes to the activation of renal pelvic mechanosensitive neurons by activating PKC. PKC increases ARNA via a PGE2-induced release of substance P.
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Feng, Huapeng, Zeng Wang, Pengyang Zhu, Li Wu, Jianzhong Shi, Yanbing Li, Jianhong Shu, Yulong He, and Huihui Kong. "ARNT Inhibits H5N1 Influenza A Virus Replication by Interacting with the PA Protein." Viruses 14, no. 7 (June 21, 2022): 1347. http://dx.doi.org/10.3390/v14071347.
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Increasing evidence suggests that the polymerase acidic (PA) protein of influenza A viruses plays an important role in viral replication and pathogenicity. However, information regarding the interaction(s) of host factors with PA is scarce. By using a yeast two-hybrid screen, we identified a novel host factor, aryl hydrocarbon receptor nuclear translocator (ARNT), that interacts with the PA protein of the H5N1 virus. The interaction between PA and human ARNT was confirmed by co-immunoprecipitation and immunofluorescence microscopy. Moreover, overexpression of ARNT downregulated the polymerase activity and inhibited virus propagation, whereas knockdown of ARNT significantly increased the polymerase activity and virus replication. Mechanistically, overexpression of ARNT resulted in the accumulation of PA protein in the nucleus and inhibited both the replication and transcription of the viral genome. Interaction domain mapping revealed that the bHLH/PAS domain of ARNT mainly interacted with the C-terminal domain of PA. Together, our results demonstrate that ARNT inhibits the replication of the H5N1 virus and could be a target for the development of therapeutic strategies against H5N1 influenza viruses.
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Okino, S. T., and J. P. Whitlock. "Dioxin induces localized, graded changes in chromatin structure: implications for Cyp1A1 gene transcription." Molecular and Cellular Biology 15, no. 7 (July 1995): 3714–21. http://dx.doi.org/10.1128/mcb.15.7.3714.
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In mouse hepatoma cells, the environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD, or dioxin) induces Cyp1A1 gene transcription, a process that requires two basic helix-loop-helix regulatory proteins, the aromatic hydrocarbon receptor (AhR) and the aromatic hydrocarbon receptor nuclear translocator (Arnt). We have used a ligation-mediated PCR technique to analyze dioxin-induced changes in protein-DNA interactions and chromatin structure of the Cyp1A1 enhancer-promoter in its native chromosomal setting. Dioxin-induced binding of the AhR/Arnt heteromer to enhancer chromatin is associated with a localized (about 200 bp) alteration in chromatin structure that is manifested by increased accessibility of the DNA; these changes probably reflect direct disruption of a nucleosome by AhR/Arnt. Dioxin induces analogous AhR/Arnt-dependent changes in chromatin structure and accessibility at the Cyp1A1 promoter. However, the changes at the promoter must occur by a different, more indirect mechanism, because they are induced from a distance and do not reflect a local effect of AhR/Arnt binding. Dose-response experiments indicate that the changes in chromatin structure at the enhancer and promoter are graded and mirror the graded induction of Cyp1A1 transcription by dioxin. We discuss these results in terms of a TCDD-induced shift in an equilibrium between nucleosomal and nonnucleosomal chromatin configurations.
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Liu, Yanli, Yifeng Yin, Yunyang Song, Kang Wang, Fanghui Wu, and Hui Jiang. "α-Conotoxin as Potential to α7-nAChR Recombinant Expressed in Escherichia coli." Marine Drugs 18, no. 8 (August 12, 2020): 422. http://dx.doi.org/10.3390/md18080422.
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α7 nicotinic acetylcholine receptors (nAChR) is an important nicotinic acetylcholine receptors subtype and closely associated with cognitive disorders, such as Alzheimer’s and schizophrenia disease. The mutant ArIB (V11L, V16A) of α-conotoxin ArIB with 17-amino acid residues specifically targets α7 nAChR with no obvious effect on other nAChR subtypes. In the study, the synthetic gene encoding mature peptide of ArIB and mutant ArIB (V11L, V16A) carried a fusion protein Trx and 6 × His-tag was separately inserted in pET-32a (+) vector and transformed into Escherichia coli strain BL21(DE3) pLysS for expression. The expressions of Trx-ArIB-His6 and Trx-ArIB (V11L, V16A)-His6 were soluble in Escherichia coli, which were purified by Ni-NTA affinity chromatography column and cleaved by enterokinase to release rArIB and rArIB (V11L, V16A). Then, rArIB and rArIB (V11L, V16A) were purified by high-performance liquid chromatography (HPLC) and identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Bioactivity of rArIB and rArIB (V11L, V16A) was assessed by two-electrode voltage-clamp electrophysiology in Xenopus laevis oocytes expressing human nAChR subtypes. The results indicated that the yield of the fusion proteins was approximately 50 mg/L and rArIB (V11L, V16A) antagonized the α7 nAChR subtype selectively with 8-nM IC50. In summary, this study provides an efficient method to biosynthesize α-conotoxin ArIB and rArIB (V11L, V16A) in Escherichia coli, which could be economical to obtain massively bioactive disulfide-rich polypeptides at fast speed.
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Nomura, Norimichi, Yoshihiko Sako, and Aritsune Uchida. "Molecular Characterization and Postsplicing Fate of Three Introns within the Single rRNA Operon of the Hyperthermophilic ArchaeonAeropyrum pernix K1." Journal of Bacteriology 180, no. 14 (July 15, 1998): 3635–43. http://dx.doi.org/10.1128/jb.180.14.3635-3643.1998.
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ABSTRACT The single rRNA operon (arnS-arnL) of the hyperthermophilic archaeon Aeropyrum pernix K1 was sequenced. The DNA sequence data and detailed RNA analyses disclosed an unusual feature: the presence of three introns at hitherto undescribed insertion positions within the rRNA genes. The 699-nucleotide (nt) intron Iα was located at position 908 (Escherichia coli numbering [H. F. Noller, Annu. Rev. Biochem. 53:119–162, 1984]) of the 16S rRNA, while the 202-nt intron Iβ and 575-nt intron Iγ were located at positions 1085 and 1927 (E. coli numbering), respectively, of the 23S rRNA. They were located within highly conserved sites which have been implicated as crucial for rRNA function in E. coli. All three introns were remarkably AT rich (41.5 to 43.1 mol% G+C) compared with the mature rRNAs (67.7 and 69.2 mol% G+C for 16S and 23S rRNAs, respectively). No obvious primary sequence similarities were detected among them. After splicing from rRNA transcripts in vivo, a large quantity of intronic RNAs were stably retained in the linear monomeric form, whereas a trace of topoisomeric RNA molecules also appeared, as characterized by their behavior in two-dimensional gel electrophoresis. Secondary structural models of the Iα-, Iβ-, and Iγ-containing rRNA precursors agree with the bulge-helix-bulge motif. Two of the introns, Iα and Iγ, contained open reading frames whose protein translation exhibited no overall similarity with proteins reported so far. However, both share a LAGLI-DADG motif characteristic of homing endonucleases.
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Williams, Selena Joy, Chunhong Gu, Joelle dela Paz, Rena Buckstein, and Richard A. Wells. "ARNT/HIF-1β: An AML Biomarker?" Blood 116, no. 21 (November 19, 2010): 2903. http://dx.doi.org/10.1182/blood.v116.21.2903.2903.
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Abstract Abstract 2903 Background: Despite improvements in chemotherapy protocols and bone marrow transplantation techniques, AML remains a lethal disease. Although patients with AML typically respond well to initial therapy, the majority relapse and eventually succumb to the disease. This relapse is thought to be the result of the resistance of leukaemic stem cells to the effects of chemotherapy. Some mechanisms have been discovered which contribute to resistance, but this phenomenon remains incompletely understood and is a significant barrier to improving patient outcomes. TEL is a member of the ETS transcription factor gene family and is essential for developmental processes such as haematopoiesis. TEL is frequently targeted by chromosomal translocations in human malignancies, resulting in the expression of oncogenic TEL gene fusions. A TEL-ARNT gene fusion was reported in a single case of AML, FAB subtype M2, in a patient whose leukaemic cells contained the balanced translocation t(1;12)(q21;p13). ARNT (also known as HIF-1β) is a nuclear protein and functions as part of a heterodimer, whose partners include HIF-1α and the aryl hydrocarbon receptor (AhR). HIF-1 expression is commonly deregulated in cancer and AhR signalling has been linked to leukaemogenesis. Materials and Results: Immunoblot analysis of patient bone marrow mononuclear cell lysates revealed that 5 of 29 AML specimens (∼17%) had elevated levels of ARNT protein, whereas 0 of 19 MDS specimens showed ARNT expression. In addition, AML specimens that had elevated ARNT protein levels also had elevated levels of phosphorylated Akt, while AML specimens that did not have elevated ARNT protein expression did not have activation of Akt signaling. Intriguingly, ARNT expression was noted in one patient who had progressed from MDS to AML. We then studied the expression of ARNT in HL60 cells, which are highly sensitive to induction of apoptosis by troglitazone (TG), and in U937 cells, which are TG resistant. In HL60 cells, ARNT mRNA levels remained constant following TG treatment and ARNT protein levels markedly decreased, while in U937 cells, ARNT mRNA levels increased and ARNT protein levels remained constant. We then tested the effect of exogenous expression of ARNT on the sensitivity of HL-60 cells to apoptosis induced by TG, daunorubin and hydrogen peroxide. HL-60 cells transduced with a retrovirus expressing ARNT became resistant to the induction of apoptosis by all these agents. These cells also had constitutive activation of Akt signaling, and treatment of these cells with a specific inhibitor of Akt signaling reversed their resistance to TG-induced apoptosis. Conclusions: The expression of ARNT confers resistance to apoptosis in AML cell lines and activates Akt signalling. In addition, ARNT is overexpressed in a significant subset of AML patients, in whom it activated Akt signaling, and ARNT expression correlates with progression of MDS to AML. ARNT may play an important role in chemoresistance and may be useful as a predictive or prognostic biomarker. Disclosures: No relevant conflicts of interest to declare.
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Soshilov, Anatoly A., Stefano Motta, Laura Bonati, and Michael S. Denison. "Transitional States in Ligand-Dependent Transformation of the Aryl Hydrocarbon Receptor into Its DNA-Binding Form." International Journal of Molecular Sciences 21, no. 7 (April 2, 2020): 2474. http://dx.doi.org/10.3390/ijms21072474.
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The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that mediates the biological and toxicological effects of an AhR lacking the entire PASB structurally diverse chemicals, including halogenated aromatic hydrocarbons. Ligand-dependent transformation of the AhR into its DNA binding form involves a ligand-dependent conformational change, heat shock protein 90 (hsp90), dissociation from the AhR complex and AhR dimerization with the AhR nuclear translocator (ARNT) protein. The mechanism of AhR transformation was examined using mutational approaches and stabilization of the AhR:hsp90 complex with sodium molybdate. Insertion of a single mutation (F281A) in the hsp90-binding region of the AhR resulted in its constitutive (ligand-independent) transformation/DNA binding in vitro. Mutations of AhR residues within the Arg-Cys-rich region (R212A, R217A, R219A) and Asp371 (D371A) impaired AhR transformation without a significant effect on ligand binding. Stabilization of AhR:hsp90 binding with sodium molybdate decreased transformation/DNA binding of the wild type AhR but had no effect on constitutively active AhR mutants. Interestingly, transformation of the AhR in the presence of molybdate allowed detection of an intermediate transformation ternary complex containing hsp90, AhR, and ARNT. These results are consistent with a stepwise transformation mechanism in which binding of ARNT to the liganded AhR:hsp90 complex results in a progressive displacement of hsp90 and conversion of the AhR into its high affinity DNA binding form. The available molecular insights into the signaling mechanism of other Per-ARNT-Sim (PAS) domains and structural information on hsp90 association with other client proteins are consistent with the proposed transformation mechanism of the AhR.
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Torii, Satoru, Shuya Kasai, Tatsushi Yoshida, Ken-ichi Yasumoto, and Shigeomi Shimizu. "Mitochondrial E3 Ubiquitin Ligase Parkin: Relationships with Other Causal Proteins in Familial Parkinson’s Disease and Its Substrate-Involved Mouse Experimental Models." International Journal of Molecular Sciences 21, no. 4 (February 11, 2020): 1202. http://dx.doi.org/10.3390/ijms21041202.
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Parkinson’s disease (PD) is a common neurodegenerative disorder. Recent identification of genes linked to familial forms of PD has revealed that post-translational modifications, such as phosphorylation and ubiquitination of proteins, are key factors in disease pathogenesis. In PD, E3 ubiquitin ligase Parkin and the serine/threonine-protein kinase PTEN-induced kinase 1 (PINK1) mediate the mitophagy pathway for mitochondrial quality control via phosphorylation and ubiquitination of their substrates. In this review, we first focus on well-characterized PINK1 phosphorylation motifs. Second, we describe our findings concerning relationships between Parkin and HtrA2/Omi, a protein involved in familial PD. Third, we describe our findings regarding inhibitory PAS (Per/Arnt/Sim) domain protein (IPAS), a member of PINK1 and Parkin substrates, involved in neurodegeneration during PD. IPAS is a dual-function protein involved in transcriptional repression of hypoxic responses and the pro-apoptotic activities.
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Maresca, Bruno, and Jeffrey H. Schwartz. "Sudden origins: A general mechanism of evolution based on stress protein concentration and rapid environmental change." Anatomical Record Part B: The New Anatomist 289B, no. 1 (January 2006): 38–46. http://dx.doi.org/10.1002/ar.b.20089.
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Coller, BS, U. Seligsohn, SM West, LE Scudder, and KJ Norton. "Platelet fibrinogen and vitronectin in Glanzmann thrombasthenia: evidence consistent with specific roles for glycoprotein IIb/IIIA and alpha v beta 3 integrins in platelet protein trafficking [see comments]." Blood 78, no. 10 (November 15, 1991): 2603–10. http://dx.doi.org/10.1182/blood.v78.10.2603.2603.
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Abstract To assess the individual contributions of the platelet glycoprotein (GP) IIb/IIIa receptor and the alpha v beta 3 vitronectin receptor to platelet levels of fibrinogen and vitronectin, we analyzed the platelets from two groups of Glanzmann thrombasthenic patients: Iraqi- Jews, whose platelets lack both receptors, and Arab patients in Israel, whose platelets lack GPIIb/IIIa, but have normal or increased numbers of alpha v beta 3 vitronectin receptors. The platelets from both thrombasthenic groups had profound deficiencies of fibrinogen, but the defect in the Iraqi-Jewish patients' platelets appeared to be slightly more severe. This finding indicates that GPIIb/IIIa is the major determinant of platelet fibrinogen, presumably acting by receptor- mediated uptake, and that the alpha v beta 3 vitronectin receptor plays little or no role. Arab patients' platelets have normal amounts of platelet vitronectin, whereas Iraqi-Jewish patients' platelets have nearly five times as much vitronectin as control or Arab patients' platelets. To account for these data, we propose a working hypothesis in which vitronectin is synthesized in megakaryocytes and the alpha v beta 3 vitronectin receptor is involved in transport of the protein out of megakaryocytes and/or platelets. Collectively, these observations suggest that in addition to their recognized roles in cell adhesion and in the interaction of cells with extracellular proteins, integrin receptors may be important in protein trafficking into, and perhaps out of, platelets.
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Coller, BS, U. Seligsohn, SM West, LE Scudder, and KJ Norton. "Platelet fibrinogen and vitronectin in Glanzmann thrombasthenia: evidence consistent with specific roles for glycoprotein IIb/IIIA and alpha v beta 3 integrins in platelet protein trafficking [see comments]." Blood 78, no. 10 (November 15, 1991): 2603–10. http://dx.doi.org/10.1182/blood.v78.10.2603.bloodjournal78102603.
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To assess the individual contributions of the platelet glycoprotein (GP) IIb/IIIa receptor and the alpha v beta 3 vitronectin receptor to platelet levels of fibrinogen and vitronectin, we analyzed the platelets from two groups of Glanzmann thrombasthenic patients: Iraqi- Jews, whose platelets lack both receptors, and Arab patients in Israel, whose platelets lack GPIIb/IIIa, but have normal or increased numbers of alpha v beta 3 vitronectin receptors. The platelets from both thrombasthenic groups had profound deficiencies of fibrinogen, but the defect in the Iraqi-Jewish patients' platelets appeared to be slightly more severe. This finding indicates that GPIIb/IIIa is the major determinant of platelet fibrinogen, presumably acting by receptor- mediated uptake, and that the alpha v beta 3 vitronectin receptor plays little or no role. Arab patients' platelets have normal amounts of platelet vitronectin, whereas Iraqi-Jewish patients' platelets have nearly five times as much vitronectin as control or Arab patients' platelets. To account for these data, we propose a working hypothesis in which vitronectin is synthesized in megakaryocytes and the alpha v beta 3 vitronectin receptor is involved in transport of the protein out of megakaryocytes and/or platelets. Collectively, these observations suggest that in addition to their recognized roles in cell adhesion and in the interaction of cells with extracellular proteins, integrin receptors may be important in protein trafficking into, and perhaps out of, platelets.
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Rojas, Vicente, Francisco Salinas, Andrés Romero, Luis F. Larrondo, and Paulo Canessa. "Interactions between Core Elements of the Botrytis cinerea Circadian Clock Are Modulated by Light and Different Protein Domains." Journal of Fungi 8, no. 5 (May 6, 2022): 486. http://dx.doi.org/10.3390/jof8050486.
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Botrytis cinerea possesses a complex light-sensing system composed of eleven photoreceptors. In B. cinerea, bcwcl1 encodes for the BcWCL1 protein, the orthologue of the blue-light photoreceptor WC-1 from Neurospora crassa. The functional partner of BcWCL1 is the BcWCL2 protein, both interacting in the nucleus and forming the B. cinerea white collar complex (BcWCC). This complex is required for photomorphogenesis and circadian regulation. However, no molecular evidence shows a light-dependent interaction between the BcWCC components or light-sensing capabilities in BcWCL1. In this work, by employing a yeast two-hybrid system that allows for the in vivo analysis of protein–protein interactions, we confirm that BcWCL1 and BcWCL2 interact in the absence of light as well as upon blue-light stimulation, primarily through their PAS (Per-Arnt-Sim) domains. Deletion of the PAS domains present in BcWCL1 (BcWCL1PAS∆) or BcWCL2 (BcWCL2PAS∆) severely impairs the interaction between these proteins. Interestingly, the BcWCL1PAS∆ protein shows a blue-light response and interacts with BcWCL2 or BcWCL2PAS∆ upon light stimulation. Finally, we demonstrate that BcWCL1 and BcWCL1PAS∆ respond to blue light by introducing a point mutation in the photoactive cysteine, confirming that both proteins are capable of light sensing. Altogether, the results revealed the complexity of protein–protein interactions occurring between the core elements of the B. cinerea circadian clock.
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Reisz-Porszasz, S., M. R. Probst, B. N. Fukunaga, and O. Hankinson. "Identification of functional domains of the aryl hydrocarbon receptor nuclear translocator protein (ARNT)." Molecular and Cellular Biology 14, no. 9 (September 1994): 6075–86. http://dx.doi.org/10.1128/mcb.14.9.6075-6086.1994.
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The activated aryl hydrocarbon receptor (AHR) and the AHR nuclear translocator (ARNT) bind DNA as a heterodimer. Both proteins represent a novel class of basic helix-loop-helix (bHLH)-containing transcription factors in that (i) activation of AHR requires the binding of ligand (e.g., 2,3,7,8-tetrachlorodibenzo-p-dioxin [TCDD]), (ii) the xenobiotic responsive element (XRE) recognized by the AHR/ARNT heterodimer differs from the recognition sequence for nearly all other bHLH proteins, and (iii) both proteins contain a PAS homology region, which in the Drosophila PER and SIM proteins functions as a dimerization domain. A cDNA for mouse ARNT has been cloned, and potential functional domains of ARNT were investigated by deletion analysis. A mutant lacking all regions of ARNT other than the bHLH and PAS regions is unimpaired in TCDD-dependent dimerization and subsequent XRE binding and only modestly reduced in ability to complement an ARNT-deficient mutant cell line, c4, in vivo. Both the first and second alpha helices of the bHLH region are required for dimerization. The basic region is required for XRE binding but not for dimerization. Deletion of either the A or B segments of the PAS region slightly affects TCDD-induced heterodimerization, while deletion of the complete PAS region severely affects (but does not eliminate) dimerization. Thus, ARNT possesses multiple domains required for maximal heterodimerization. Mutants deleted for PAS A, PAS B, and the complete PAS region all retain some degree of XRE binding, yet none can rescue the c4 mutant. Therefore, both the PAS A and PAS B segments, besides contributing to dimerization, apparently fulfill additional, unknown functions required for biological activity of ARNT.
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Reisz-Porszasz, S., M. R. Probst, B. N. Fukunaga, and O. Hankinson. "Identification of functional domains of the aryl hydrocarbon receptor nuclear translocator protein (ARNT)." Molecular and Cellular Biology 14, no. 9 (September 1994): 6075–86. http://dx.doi.org/10.1128/mcb.14.9.6075.
Full textAbstract:
The activated aryl hydrocarbon receptor (AHR) and the AHR nuclear translocator (ARNT) bind DNA as a heterodimer. Both proteins represent a novel class of basic helix-loop-helix (bHLH)-containing transcription factors in that (i) activation of AHR requires the binding of ligand (e.g., 2,3,7,8-tetrachlorodibenzo-p-dioxin [TCDD]), (ii) the xenobiotic responsive element (XRE) recognized by the AHR/ARNT heterodimer differs from the recognition sequence for nearly all other bHLH proteins, and (iii) both proteins contain a PAS homology region, which in the Drosophila PER and SIM proteins functions as a dimerization domain. A cDNA for mouse ARNT has been cloned, and potential functional domains of ARNT were investigated by deletion analysis. A mutant lacking all regions of ARNT other than the bHLH and PAS regions is unimpaired in TCDD-dependent dimerization and subsequent XRE binding and only modestly reduced in ability to complement an ARNT-deficient mutant cell line, c4, in vivo. Both the first and second alpha helices of the bHLH region are required for dimerization. The basic region is required for XRE binding but not for dimerization. Deletion of either the A or B segments of the PAS region slightly affects TCDD-induced heterodimerization, while deletion of the complete PAS region severely affects (but does not eliminate) dimerization. Thus, ARNT possesses multiple domains required for maximal heterodimerization. Mutants deleted for PAS A, PAS B, and the complete PAS region all retain some degree of XRE binding, yet none can rescue the c4 mutant. Therefore, both the PAS A and PAS B segments, besides contributing to dimerization, apparently fulfill additional, unknown functions required for biological activity of ARNT.
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Labrecque, M., G. Prefontaine, and T. Beischlag. "The Aryl Hydrocarbon Receptor Nuclear Translocator (ARNT) Family of Proteins: Transcriptional Modifiers with Multi-Functional Protein Interfaces." Current Molecular Medicine 13, no. 7 (July 1, 2013): 1047–65. http://dx.doi.org/10.2174/15665240113139990042.
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Robichon, Carine, Jianying Luo, Thomas B. Causey, Jack S. Benner, and James C. Samuelson. "Engineering Escherichia coli BL21(DE3) Derivative Strains To Minimize E. coli Protein Contamination after Purification by Immobilized Metal Affinity Chromatography." Applied and Environmental Microbiology 77, no. 13 (May 20, 2011): 4634–46. http://dx.doi.org/10.1128/aem.00119-11.
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ABSTRACTRecombinant His-tagged proteins expressed inEscherichia coliand purified by immobilized metal affinity chromatography (IMAC) are commonly coeluted with nativeE. coliproteins, especially if the recombinant protein is expressed at a low level. TheE. colicontaminants display high affinity to divalent nickel or cobalt ions, mainly due to the presence of clustered histidine residues or biologically relevant metal binding sites. To improve the final purity of expressed His-tagged protein, we engineeredE. coliBL21(DE3) expression strains in which the most recurring contaminants are either expressed with an alternative tag or mutated to decrease their affinity to divalent cations. The current study presents the design, engineering, and characterization of twoE. coliBL21(DE3) derivatives, NiCo21(DE3) and NiCo22(DE3), which express the endogenous proteins SlyD, Can, ArnA, and (optionally) AceE fused at their C terminus to a chitin binding domain (CBD) and the protein GlmS, with six surface histidines replaced by alanines. We show that eachE. coliCBD-tagged protein remains active and can be efficiently eliminated from an IMAC elution fraction using a chitin column flowthrough step, while the modification of GlmS results in loss of affinity for nickel-containing resin. The “NiCo” strains uniquely complement existing methods for improving the purity of recombinant His-tagged protein.
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Rafiq, Nisha Bte Mohd, Zi Zhao Lieu, Tingting Jiang, Cheng-han Yu, Paul Matsudaira, Gareth E. Jones, and Alexander D. Bershadsky. "Podosome assembly is controlled by the GTPase ARF1 and its nucleotide exchange factor ARNO." Journal of Cell Biology 216, no. 1 (December 22, 2016): 181–97. http://dx.doi.org/10.1083/jcb.201605104.
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Podosomes represent a class of integrin-mediated cell-matrix adhesions formed by migrating and matrix-degrading cells. We demonstrate that in macrophage-like THP1 cells and fibroblasts stimulated to produce podosomes, down-regulation of the G-protein ARF1 or the ARF1 guanine nucleotide exchange factor, ARNO, by small, interfering RNA or pharmacological inhibitors led to striking podosome elimination. Concomitantly, treatments inducing podosome formation increased the level of guanosine triphosphate (GTP)–bound ARF1. ARNO was found to colocalize with the adhesive rings of podosomes, whereas ARF1 was localized to vesicular structures transiently contacting podosome rings. Inhibition of ARF1 led to an increase in RhoA-GTP levels and triggered assembly of myosin-IIA filaments in THP1 cells, whereas the suppression of myosin-IIA rescued podosome formation regardless of ARF1 inhibition. Finally, expression of constitutively active ARF1 in fibroblasts induced formation of putative podosome precursors: actin-rich puncta coinciding with matrix degradation sites and containing proteins of the podosome core but not of the adhesive ring. Thus, ARNO-ARF1 regulates formation of podosomes by inhibition of RhoA/myosin-II and promotion of actin core assembly.
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Adhikari, Ayan, Saroj Biswas, Aditi Mukherjee, Sumit Das, and Subrata Adak. "PAS domain-containing phosphoglycerate kinase deficiency in Leishmania major results in increased autophagosome formation and cell death." Biochemical Journal 476, no. 8 (April 30, 2019): 1303–21. http://dx.doi.org/10.1042/bcj20190041.
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AbstractPer-Arnt-Sim (PAS) domains are structurally conserved and present in numerous proteins throughout all branches of the phylogenetic tree. Although PAS domain-containing proteins are major players for the adaptation to environmental stimuli in both prokaryotic and eukaryotic organisms, these types of proteins are still uncharacterized in the trypanosomatid parasites, Trypanosome and Leishmania. In addition, PAS-containing phosphoglycerate kinase (PGK) protein is uncharacterized in the literature. Here, we report a PAS domain-containing PGK (LmPAS-PGK) in the unicellular pathogen Leishmania. The modeled structure of N-terminal of this protein exhibits four antiparallel β sheets centrally flanked by α helices, which is similar to the characteristic signature of PAS domain. Activity measurements suggest that acidic pH can directly stimulate PGK activity. Localization studies demonstrate that the protein is highly enriched in the glycosome and its presence can also be seen in the lysosome. Gene knockout, overexpression and complement studies suggest that LmPAS-PGK plays a fundamental role in cell survival through autophagy. Furthermore, the knockout cells display a marked decrease in virulence when host macrophage and BALB/c mice were infected with them. Our work begins to clarify how acidic pH-dependent ATP generation by PGK is likely to function in cellular adaptability of Leishmania.
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Susianti, Susianti, Ulfah Amalia, and Laras Rianingsih. "PENAMBAHAN GUM ARAB DENGAN KONSENTRASI YANG BERBEDA TERHADAP KANDUNGAN SENYAWA VOLATIL BUBUK RUSIP IKAN TERI (Stolephorus sp.)." Jurnal Ilmu dan Teknologi Perikanan 2, no. 1 (June 8, 2020): 10–19. http://dx.doi.org/10.14710/jitpi.2020.8083.
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Rusip merupakan produk fermentasi ikan dengan menggunakan bahan baku ikan yang berukuran kecil seperti ikan teri dan memiliki aroma manis khas yang berfungsi sebagai bumbu masakan. Pengolahan rusip menjadi bubuk mengakibatkan komponen senyawa volatil dapat hilang sehingga diperlukan bahan untuk melindunginya salah satunya gum arab. Tujuan dari penelitian ini untuk mengetahui pengaruh penambahan gum arab terhadap senyawa volatil bubuk rusip dan mengetahui kandungan senyawa volatil yang terdapat pada bubuk rusip. Penelitian ini bersifat experimental laboratories model Rancangan Acak Lengkap dengan perlakuan konsentrasi gum arab yang berbeda yaitu 0%, 2,5%, 5% dan 7,5% dengan 3 kali pengulangan. Data parametrik (kadar asam glutamat, kadar protein dan kadar air) dianalisa menggunakan Anova BNJ, sedangkan data non parametrik (hedonik) menggunakan uji Kruskal Wallis. Hasil Anova BNJ menunjukkan gum arab berpengaruh terhadap bubuk rusip (P<5%) terhadap kadar asam glutamat, kadar protein dan kadar air. Penambahan gum arab terhadap senyawa volatil bubuk rusip berpengaruh terhadap kemunculan puncak dan area terbesar yaitu 62,51%. Senyawa volatil bubuk rusip dengan penambahan gum arab memberikan hasil yang lebih tinggi dengan kandungan senyawa volatil yang berasal dari golongan hidrokarbon, ester dan beberapa golongan lain seperti nitrogen. Hasil pada bubuk rusip dengan penambahan gum arab 5% merupakan perlakuan terbaik dengan kadar asam glutamat 13,44±0,06 mg, kadar protein 27,29±0,28% dan kadar air 8,24±0,03%. Tingkat penerimaan panelis terhadap bubuk rusip paling disukai pada konsentrasi 5% dengan rata-rata 8,10±0,48.
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Fong, Karen P., Ling Gao, and Donald R. Demuth. "luxS and arcB Control Aerobic Growth of Actinobacillus actinomycetemcomitans under Iron Limitation." Infection and Immunity 71, no. 1 (January 2003): 298–308. http://dx.doi.org/10.1128/iai.71.1.298-308.2003.
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ABSTRACT LuxS is responsible for the production of autoinducer 2 (AI-2), which functions in Vibrio harveyi as a quorum-sensing signal that controls the cell density-dependent expression of the lux operon. In nonluminescent organisms, the physiologic role of AI-2 is not clear. We report that inactivation of luxS in Actinobacillus actinomycetemcomitans JP2 results in reduced growth of the mutant, but not the wild-type organism, under aerobic, iron-limited conditions. Stunted cultures of the luxS mutant A. actinomycetemcomitans JP2-12 grew to high cell density when subcultured under iron-replete conditions. In addition, the mutant strain grew to high cell density under iron limitation after transformation with a plasmid containing a functional copy of luxS. Results of real-time PCR showed that A. actinomycetemcomitans JP2-12 exhibited significantly reduced expression of afuA (eightfold), fecBCDE (10-fold), and ftnAB (>50-fold), which encode a periplasmic ferric transport protein, a putative ferric citrate transporter, and ferritin, respectively. The expressions of putative receptors for transferrin, hemoglobin, and hemophore binding protein were also reduced at more modest levels (two- to threefold). In contrast, expressions of sidD and frpB (encoding putative siderophore receptors) were increased 10- and 3-fold, respectively, in the luxS mutant. To better understand the mechanism of the AI-2 response, the A. actinomycetemcomitans genome was searched for homologs of the V. harveyi signal transduction proteins, LuxP, LuxQ, LuxU, and LuxO. Interestingly, ArcB was found to be most similar to LuxQ sensor/kinase. To determine whether arcB plays a role in the response of A. actinomycetemcomitans to AI-2, an arcB-deficient mutant was constructed. The isogenic arcB mutant grew poorly under anaerobic conditions but grew normally under aerobic iron-replete conditions. However, the arcB mutant failed to grow aerobically under iron limitation, and reverse transcriptase PCR showed that inactivation of arcB resulted in decreased expression of afuA and ftnAB. Thus, isogenic luxS and arcB mutants of A. actinomycetemcomitans exhibit similar phenotypes when cultured aerobically under iron limitation, and both mutants exhibit reduced expression of a common set of genes involved in the transport and storage of iron. These results suggest that LuxS and ArcB may act in concert to control the adaptation of A. actinomycetemcomitans to iron-limiting conditions and its growth under such conditions.
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Uçar, Sema, Mahmut Çoker, and Hatice Yildirim. "Application of Biotechnologycal Methods for Removal of Phenylalanıne from Different Protein Sources." Annual Research & Review in Biology 4, no. 24 (January 10, 2014): 4529–34. http://dx.doi.org/10.9734/arrb/2014/8880.
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Assielou, Bernard, Edmond Due, Michel Koffi, Soumaila Dabonne, and Patrice Kouame. "Oryctes owariensis Larvae as Good Alternative Protein Source: Nutritional and Functional Properties." Annual Research & Review in Biology 8, no. 3 (January 10, 2015): 1–9. http://dx.doi.org/10.9734/arrb/2015/19093.
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Irmawaty, I., Tuti Widjastuti, Asep Anang, and Muhammad Nur Hidayat. "Performance Chickens Kedu, Arab and Its Cross Breeds (Poncin) Of Distribution Content Protein Of Growth Fase (Age 0 -12 Week)." Chalaza Journal of Animal Husbandry 5, no. 2 (December 31, 2020): 40–47. http://dx.doi.org/10.31327/chalaza.v5i2.1303.
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This experiment shows performance chickens of Kedu, Arab, and Poncin with Giffen different protein content. This experiment uses chickens of Kedu, Arab, and Poncin (a crossbreed of male Arab and female Kedu) that each breed consists of 40 Day Old Chicken. Each species was randomly placed in 8 units of experiment cage, and every experiment cage consists of 5 Day Old Chicken. Treatment dietary is used 15% (R1) dan 18% (R2). The experiment's design is used a completely random design 2x3 factorial, that i two treatments of dietary and three breeds of chickens. Every treatment is replayed four times, and the show used 24 units of experiment cage. The parameter is limited watch on dietary Consumption, body weight gain, and feed conversion. The result showed that Poncin chickens gave better growth performance when compared to Arab and Kedu chickens. Simultaneously, the ration protein content of 18 % resulted in better growth performance compared to 15% ration protein.
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Surajat, Asis, and Anita Mustika Ibrahim. "Pengaruh penambahan tepung daun Indigofera (Indigofera zollingeriana) dalam pakan terhadap kandungan kimia telur Ayam Arab." Jurnal Ilmu Peternakan Terapan 4, no. 2 (March 31, 2021): 66–70. http://dx.doi.org/10.25047/jipt.v4i2.2513.
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Penelitian ini bertujuan untuk mengevaluasi pengaruh penambahan tepung daun Indigofera zollingeriana terhadap kualitas kimia telur ayam arab. Penelitian dilakukan selama 3 bulan di kelompok peternakan unggas Permata Kelurahan Wua - wua, Kendari. Pengujian kandungan kolesterol, lemak, dan protein telur dilakukan di Laboratorium Terpadu Institut Pertanian Bogor. Penelitian ini menggunakan Rancangan Acak Lengkap dengan 4 perlakuan dan 4 ulangan. Ransum perlakuan menggunakan persentase tepung daun Indigofera zollingeriana yang diuji terdiri atas: P0= 0% (kontrol), P1= 10%, P2= 15%, dan P3= 20%. Parameter yang diamati adalah kadar lemak, protein, dan kolestrol telur ayam arab. Data hasil penelitian dianalisis menggunakan rancangan acak lengkap (RAL). Apabila perlakuan berpengaruh nyata maka dilakukan Uji Duncan Multiple Range Test (DMRT). Hasil penelitian menunjukan bahwa penambahan tepung daun Indigofera zollingeriana pada pakan hingga 20% tidak memberikan pengaruh yang nyata terhadap kadar protein, lemak, dan kolestrol telur Ayam Arab (P>0,05). Penggunaan tepung daun Indigofera zollingeriana sampai dengan 20% dalam pakan tidak mempengaruhi kualitas kimia telur ayam arab.