scholarly journals bHLH–PAS Proteins: Their Structure and Intrinsic Disorder

2019 ◽  
Vol 20 (15) ◽  
pp. 3653 ◽  
Author(s):  
Marta Kolonko ◽  
Beata Greb-Markiewicz
Keyword(s):  
X Ray ◽  
Intrinsically Disordered ◽  
Helix Loop Helix ◽  
Knowledge Based ◽  
Current State ◽  
Conserved Domain ◽  
Living Organisms ◽  
Nmr Methods ◽  
And Function

The basic helix–loop–helix/Per-ARNT-SIM (bHLH–PAS) proteins are a class of transcriptional regulators, commonly occurring in living organisms and highly conserved among vertebrates and invertebrates. These proteins exhibit a relatively well-conserved domain structure: the bHLH domain located at the N-terminus, followed by PAS-A and PAS-B domains. In contrast, their C-terminal fragments present significant variability in their primary structure and are unique for individual proteins. C-termini were shown to be responsible for the specific modulation of protein action. In this review, we present the current state of knowledge, based on NMR and X-ray analysis, concerning the structural properties of bHLH–PAS proteins. It is worth noting that all determined structures comprise only selected domains (bHLH and/or PAS). At the same time, substantial parts of proteins, comprising their long C-termini, have not been structurally characterized to date. Interestingly, these regions appear to be intrinsically disordered (IDRs) and are still a challenge to research. We aim to emphasize the significance of IDRs for the flexibility and function of bHLH–PAS proteins. Finally, we propose modern NMR methods for the structural characterization of the IDRs of bHLH–PAS proteins.

scholarly journals Regeneration of Planarian Auricles and Reestablishment of Chemotactic Ability

2021 ◽  
Vol 9 ◽  
Author(s):  
Eugene Matthew P. Almazan ◽  
Joseph F. Ryan ◽  
Labib Rouhana
Keyword(s):  
Molecular Mechanisms ◽  
Behavioral Experiments ◽  
X Ray ◽  
Preferential Expression ◽  
Chemical Stimuli ◽  
And Function ◽  
Function Models ◽  
Chemotactic Ability

Detection of chemical stimuli is crucial for living systems and also contributes to quality of life in humans. Since loss of olfaction becomes more prevalent with aging, longer life expectancies have fueled interest in understanding the molecular mechanisms behind the development and maintenance of chemical sensing. Planarian flatworms possess an unsurpassed ability for stem cell-driven regeneration that allows them to restore any damaged or removed part of their bodies. This includes anteriorly-positioned lateral flaps known as auricles, which have long been thought to play a central role in chemotaxis. The contribution of auricles to the detection of positive chemical stimuli was tested in this study using Girardia dorotocephala, a North American planarian species known for its morphologically prominent auricles. Behavioral experiments staged under laboratory conditions revealed that removal of auricles by amputation leads to a significant decrease in the ability of planarians to find food. However, full chemotactic capacity is observed as early as 2 days post-amputation, which is days prior from restoration of auricle morphology, but correlative with accumulation of ciliated cells in the position of auricle regeneration. Planarians subjected to x-ray irradiation prior to auricle amputation were unable to restore auricle morphology, but were still able to restore chemotactic capacity. These results indicate that although regeneration of auricle morphology requires stem cells, some restoration of chemotactic ability can still be achieved in the absence of normal auricle morphology, corroborating with the initial observation that chemotactic success is reestablished 2-days post-amputation in our assays. Transcriptome profiles of excised auricles were obtained to facilitate molecular characterization of these structures, as well as the identification of genes that contribute to chemotaxis and auricle development. A significant overlap was found between genes with preferential expression in auricles of G. dorotocephala and genes with reduced expression upon SoxB1 knockdown in Schmidtea mediterranea, suggesting that SoxB1 has a conserved role in regulating auricle development and function. Models that distinguish between possible contributions to chemotactic behavior obtained from cellular composition, as compared to anatomical morphology of the auricles, are discussed.

scholarly journals Stability and flexibility of full-length human oligodendrocytic QKI6

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Arne Raasakka ◽  
Petri Kursula
Keyword(s):  
Rna Binding ◽  
Full Length ◽  
Rna Transport ◽  
Myelin Membrane ◽  
X Ray ◽  
Intrinsically Disordered ◽  
X Ray Scattering ◽  
The Central Nervous System ◽  
Sequential Unfolding

Abstract Objective Oligodendrocytes account for myelination in the central nervous system. During myelin compaction, key proteins are translated in the vicinity of the myelin membrane, requiring targeted mRNA transport. Quaking isoform 6 (QKI6) is a STAR domain-containing RNA transport protein, which binds a conserved motif in the 3′-UTR of certain mRNAs, affecting the translation of myelination-involved proteins. RNA binding has been earlier structurally characterized, but information about full-length QKI6 conformation is lacking. Based on known domains and structure predicitons, we expected full-length QKI6 to be flexible and carry disordered regions. Hence, we carried out biophysical and structural characterization of human QKI6. Results We expressed and purified full-length QKI6 and characterized it using mass spectrometry, light scattering, small-angle X-ray scattering, and circular dichroism spectroscopy. QKI6 was monodisperse, folded, and mostly dimeric, being oxidation-sensitive. The C-terminal tail was intrinsically disordered, as predicted. In the absence of RNA, the RNA-binding subdomain is likely to present major flexibility. In thermal stability assays, a double sequential unfolding behaviour was observed in the presence of phosphate, which may interact with the RNA-binding domain. The results confirm the flexibility and partial disorder of QKI6, which may be functionally relevant.

scholarly journals Cloning and Characterization of Two Evolutionarily Conserved Subunits (TFIIIC102 and TFIIIC63) of Human TFIIIC and Their Involvement in Functional Interactions with TFIIIB and RNA Polymerase III

1999 ◽  
Vol 19 (7) ◽  
pp. 4944-4952 ◽  
Author(s):  
Yng-Ju Hsieh ◽  
Zhengxin Wang ◽  
Robert Kovelman ◽  
Robert G. Roeder
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Iii ◽  
Structure And Function ◽  
Class Iii ◽  
Tetratricopeptide Repeats ◽  
Helix Loop Helix ◽  
Polymerase Iii ◽  
And Function

ABSTRACT Human transcription factor IIIC (hTFIIIC) is a multisubunit complex that mediates transcription of class III genes through direct recognition of promoters (for tRNA and virus-associated RNA genes) or promoter-TFIIIA complexes (for the 5S RNA gene) and subsequent recruitment of TFIIIB and RNA polymerase III. We describe the cognate cDNA cloning and characterization of two subunits (hTFIIIC63 and hTFIIIC102) that are present within a DNA-binding subcomplex (TFIIIC2) of TFIIIC and are related in structure and function to two yeast TFIIIC subunits (yTFIIIC95 and yTFIIIC131) previously shown to interact, respectively, with the promoter (A box) and with a subunit of yeast TFIIIB. hTFIIIC63 and hTFIIIC102 show parallel in vitro interactions with the homologous human TFIIIB and RNA polymerase III components, as well as additional interactions that may facilitate both TFIIIB and RNA polymerase III recruitment. These include novel interactions of hTFIIIC63 with hTFIIIC102, with hTFIIIB90, and with hRPC62, in addition to the hTFIIIC102–hTFIIIB90 and hTFIIIB90–hRPC39 interactions that parallel the previously described interactions in yeast. As reported for yTFIIIC131, hTFIIIC102 contains acidic and basic regions, tetratricopeptide repeats (TPRs), and a helix-loop-helix domain, and mutagenesis studies have implicated the TPRs in interactions both with hTFIIIC63 and with hTFIIIB90. These observations further document conservation from yeast to human of the structure and function of the RNA polymerase III transcription machinery, but in addition, they provide new insights into the function of hTFIIIC and suggest direct involvement in recruitment of both TFIIIB and RNA polymerase III.

Darstellung und Charakterisierung von Spezies der Zusammensetzung η5-C5H5Cr(NO)2SR (R = C6H5, C6F5, t–C4H9) und [η5-C5H5CrNO]2(ER)2 (E = O, S, Se, Te, R = Alkyl, Aryl); Röntgenstrukturanalysen von [η5-C5H5(NO)Cr(μ-SeC6H5)2Cr(NO)-η5-C5H5] und [η5-C5H5(NO)Cr(μ-Se-n-C4H9)(μ-OH)Cr(NO)-η5-C5H5] / Synthesis and Characterization of Species of Composition η5-C5H5Cr(NO)2SR (R = C6H5, C6F5, t-C4H9) and [η5-C5H5CrNO]2(ER)2 (E = O, S, Se, Te, R = Alkyl, Aryl); Röntgenstrukturanalysen von [η5-C5H5(NO)Cr(μ-SeC6H5)2Cr(NO)-η5-C5H5] and [η5-C5H5(NO)Cr(μ-Se-n-C4H9)(μ-OH)Cr(NO)-η5-C5H5]

1982 ◽  
Vol 37 (1) ◽  
pp. 13-23 ◽  
Author(s):  
Johannes Rott ◽  
Ernst Guggolz ◽  
Albert Rettenmeier ◽  
Manfred L. Ziegler
Keyword(s):  
Mass Spectra ◽  
Membered Ring ◽  
Molecular Structures ◽  
Binuclear Complexes ◽  
Alkyl Aryl ◽  
X Ray ◽  
H Nmr ◽  
Crystal And Molecular Structures ◽  
Nmr Methods

The title compounds have been synthesized and characterized by elemental analysis, IR and 1H NMR methods and mass spectra. The crystal and molecular structures of the binuclear complexes [η-C5H5(NO)Cr(μ-SeC6H5)2Cr(NO)-η5-C5H5] and [η5-C5H5(NO)Crμ-Se-n-C4H9)(μ-OH)Cr(NO)-μ5-C5H5] have been determined by X-ray structure analysis. The latter is shown to have a four-membered ring consisting of two chromium atoms, one selenium, and one oxygen atom.

scholarly journals The CLU-files: disentanglement of a mystery

2016 ◽  
Vol 7 (1) ◽  
pp. 1-15 ◽  
Author(s):  
Philipp Rohne ◽  
Hans Prochnow ◽  
Claudia Koch-Brandt
Keyword(s):  
Molecular Chaperone ◽  
Cell Biology ◽  
Protein S ◽  
Subcellular Location ◽  
Current State ◽  
Apolipoprotein J ◽  
Health And Disease ◽  
Molecular Cell Biology ◽  
And Function

AbstractThe multifaceted protein clusterin (CLU) has been challenging researchers for more than 35 years. The characterization of CLU as a molecular chaperone was one of the major breakthroughs in CLU research. Today, secretory clusterin (sCLU), also known as apolipoprotein J (apoJ), is considered one of the most important extracellular chaperones ever found. It is involved in a broad range of physiological and pathophysiological functions, where it exerts a cytoprotective role. Descriptions of various forms of intracellular CLU have led to further and even contradictory functions. To untangle the current state of knowledge of CLU, this review will combine old views in the field, with new discoveries to highlight the nature and function of this fascinating protein(s). In this review, we further describe the expression and subcellular location of various CLU forms. Moreover, we discuss recent insights into the structure of CLU and assess how structural properties as well as the redox environment determine the chaperone activity of CLU. Eventually, the review connects the biochemistry and molecular cell biology of CLU with medical aspects, to formulate a hypothesis of a CLU function in health and disease.

scholarly journals Subcellular Localization Signals of bHLH-PAS Proteins: Their Significance, Current State of Knowledge and Future Perspectives

2019 ◽  
Vol 20 (19) ◽  
pp. 4746
Author(s):  
Beata Greb-Markiewicz ◽  
Marta Kolonko
Keyword(s):  
Transcription Factors ◽  
Nuclear Export ◽  
Protein Localization ◽  
Nuclear Localization Signals ◽  
Extracellular Signals ◽  
Helix Loop Helix ◽  
Current State ◽  
Activation Of Transcription ◽  
Living Organisms ◽  
Current Stage

The bHLH-PAS (basic helix-loop-helix/ Period-ARNT-Single minded) proteins are a family of transcriptional regulators commonly occurring in living organisms. bHLH-PAS members act as intracellular and extracellular “signals” sensors, initiating response to endo- and exogenous signals, including toxins, redox potential, and light. The activity of these proteins as transcription factors depends on nucleocytoplasmic shuttling: the signal received in the cytoplasm has to be transduced, via translocation, to the nucleus. It leads to the activation of transcription of particular genes and determines the cell response to different stimuli. In this review, we aim to present the current state of knowledge concerning signals that affect shuttling of bHLH-PAS transcription factors. We summarize experimentally verified and published nuclear localization signals/nuclear export signals (NLSs/NESs) in the context of performed in silico predictions. We have used most of the available NLS/NES predictors. Importantly, all our results confirm the existence of a complex system responsible for protein localization regulation that involves many localization signals, which activity has to be precisely controlled. We conclude that the current stage of knowledge in this area is still not complete and for most of bHLH-PAS proteins an experimental verification of the activity of further NLS/NES is needed.

scholarly journals Characterization of Microbial Degradation Products of Steviol Glycosides

Molecules ◽  
2021 ◽  
Vol 26 (22) ◽  
pp. 6916
Author(s):  
Gert Steurs ◽  
Nico Moons ◽  
Luc Van Meervelt ◽  
Boudewijn Meesschaert ◽  
Wim Michel De Borggraeve
Keyword(s):  
Chemical Synthesis ◽  
Microbial Degradation ◽  
Degradation Products ◽  
Reduced Form ◽  
Steviol Glycosides ◽  
X Ray ◽  
Incubation Experiments ◽  
Tricyclic Ketone ◽  
Nmr Methods

Steviol glycosides were subjected to bacteria present in a soil sample collected from a Stevia plantation in Paraguay. During the incubation experiments, next to the aglycon steviol, steviol degradation products were also formed. X-ray analysis and NMR methods in combination with chemical synthesis and GIAO NMR calculations were used to fully characterize the structure of these compounds as a tricyclic ketone and the corresponding reduced form. They were nicknamed monicanone and monicanol. The latter has the (S)-configuration at the alcohol site.

scholarly journals Advanced ensemble modelling of flexible macromolecules using X-ray solution scattering

IUCrJ ◽  
2015 ◽  
Vol 2 (2) ◽  
pp. 207-217 ◽  
Author(s):  
Giancarlo Tria ◽  
Haydyn D. T. Mertens ◽  
Michael Kachala ◽  
Dmitri I. Svergun
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Conformational Space ◽  
Disordered Proteins ◽  
Biological Macromolecules ◽  
Flexible Systems ◽  
Saxs Data ◽  
X Ray ◽  
Intrinsically Disordered ◽  
Ensemble Optimization

Dynamic ensembles of macromolecules mediate essential processes in biology. Understanding the mechanisms driving the function and molecular interactions of `unstructured' and flexible molecules requires alternative approaches to those traditionally employed in structural biology. Small-angle X-ray scattering (SAXS) is an established method for structural characterization of biological macromolecules in solution, and is directly applicable to the study of flexible systems such as intrinsically disordered proteins and multi-domain proteins with unstructured regions. TheEnsemble Optimization Method(EOM) [Bernadóet al.(2007).J. Am. Chem. Soc.129, 5656–5664] was the first approach introducing the concept of ensemble fitting of the SAXS data from flexible systems. In this approach, a large pool of macromolecules covering the available conformational space is generated and a sub-ensemble of conformers coexisting in solution is selected guided by the fit to the experimental SAXS data. This paper presents a series of new developments and advancements to the method, including significantly enhanced functionality and also quantitative metrics for the characterization of the results. Building on the original concept of ensemble optimization, the algorithms for pool generation have been redesigned to allow for the construction of partially or completely symmetric oligomeric models, and the selection procedure was improved to refine the size of the ensemble. Quantitative measures of the flexibility of the system studied, based on the characteristic integral parameters of the selected ensemble, are introduced. These improvements are implemented in the newEOMversion 2.0, and the capabilities as well as inherent limitations of the ensemble approach in SAXS, and ofEOM2.0 in particular, are discussed.

scholarly journals Oil Palm Phytochrome-Interacting Factor4 (PIF4) Gene is Conserved and Highly Expressed During Somatic Embryogenesis

2019 ◽  
Vol 26 (4) ◽  
pp. 172
Author(s):  
Mantira Suksirt ◽  
Kamolwan Khianchaikhan ◽  
Mya Thuzar ◽  
Supachai Vuttipongchaikij ◽  
Chatchawan Jantasuriyarat
Keyword(s):  
Tissue Culture ◽  
Somatic Embryogenesis ◽  
Oil Palm ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Conserved Domain ◽  
Long Time ◽  
Pcr Method ◽  
High Level

Oil palm is used in food, fuel and cosmetic industries. Tissue culture is the best way to propagate oil palm; unfortunately the somatic embryogenesis during tissue culture takes long time. The molecular mechanism of somatic embryogenesis in oil palm remains unknown. Recent research reported that auxin plays an important role in early and post-embryogenic plant. PHYTOCHROME-INTERACTING FACTOR4 (PIF4) regulates levels of auxin and the expression of key auxin biosynthesis genes. Our research aims to characterize oil palm PIF4 gene. Thus, we cloned EgPIF4, analyzed the domain using bioinformatic and examined the expression of EgPIF4 during somatic embryogenesis at different tissue including callus and somatic embryo stages; globular, torpedo, cotyledon, and plantlet stage using real-time PCR method. The result showed that EgPIF4 gene comprised 1,737 bp with 9 exons, which encode 578 amino acid residuals. It contains a conserved domain called basic helix-loop-helix domain. EgPIF4 has high level of expression at somatic embryogenetic stage specifically globular and torpedo stage suggested that EgPIF4 plays an important role during somatic embryogenesis. The future characterization of EgPIF4 function in oil palm will help to understand somatic embryogenesis process and facilitate the improvement of the oil palm tissue culture.

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