Mutational analysis of Mdm2 C-terminal tail suggests an evolutionarily conserved role of its length in Mdm2 activity toward p53 and indicates structural differences between Mdm2 homodimers and Mdm2/MdmX heterodimers

AbstractHistone H2AK119 mono-ubiquitination (H2AK119Ub) is a relatively abundant histone modification, mainly catalyzed by the Polycomb Repressive Complex 1 (PRC1) to regulate Polycomb-mediated transcriptional repression of downstream target genes. Consequently, H2AK119Ub can also be dynamically reversed by the BAP1 complex, an evolutionarily conserved multiprotein complex that functions as a general transcriptional activator. In previous studies, it has been reported that the BAP1 complex consists of important biological roles in development, metabolism, and cancer. However, identifying the BAP1 complex’s regulatory mechanisms remains to be elucidated due to its various complex forms and its ability to target non-histone substrates. In this review, we will summarize recent findings that have contributed to the diverse functional role of the BAP1 complex and further discuss the potential in targeting BAP1 for therapeutic use.

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The folate-binding module ofThermus thermophiluscobalamin-dependent methionine synthase displays a distinct variation of the classical TIM barrel: a TIM barrel with a `twist'

Acta Crystallographica Section D Structural Biology ◽

10.1107/s2059798317018290 ◽

2018 ◽

Vol 74 (1) ◽

pp. 41-51

Author(s):

Kazuhiro Yamada ◽

Markos Koutmos

Keyword(s):

Tertiary Amine ◽

Thermus Thermophilus ◽

Methionine Synthase ◽

Structural Studies ◽

Binding Domains ◽

Methyl Transfer ◽

Structural Differences ◽

Tim Barrel ◽

Eukaryotic Organisms

Methyl transfer between methyltetrahydrofolate and corrinoid molecules is a key reaction in biology that is catalyzed by a number of enzymes in many prokaryotic and eukaryotic organisms. One classic example of such an enzyme is cobalamin-dependent methionine synthase (MS). MS is a large modular protein that utilizes an SN2-type mechanism to catalyze the chemically challenging methyl transfer from the tertiary amine (N5) of methyltetrahydrofolate to homocysteine in order to form methionine. Despite over half a century of study, many questions remain about how folate-dependent methyltransferases, and MS in particular, function. Here, the structure of the folate-binding (Fol) domain of MS fromThermus thermophilusis reported in the presence and absence of methyltetrahydrofolate. It is found that the methyltetrahydrofolate-binding environment is similar to those of previously described methyltransferases, highlighting the conserved role of this domain in binding, and perhaps activating, the methyltetrahydrofolate substrate. These structural studies further reveal a new distinct and uncharacterized topology in the C-terminal region of MS Fol domains. Furthermore, it is found that in contrast to the canonical TIM-barrel β8α8fold found in all other folate-binding domains, MS Fol domains exhibit a unique β8α7fold. It is posited that these structural differences are important for MS function.

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MicroRNAs in Cardiac Autophagy: Small Molecules and Big Role

Cells ◽

10.3390/cells7080104 ◽

2018 ◽

Vol 7 (8) ◽

pp. 104 ◽

Cited By ~ 22

Author(s):

Teng Sun ◽

Meng-Yang Li ◽

Pei-Feng Li ◽

Ji-Min Cao

Keyword(s):

Cardiac Fibrosis ◽

Heart Diseases ◽

Critical Role ◽

Transcriptional Gene Silencing ◽

Close Link ◽

Post Transcriptional Gene Silencing ◽

Evolutionarily Conserved ◽

Cardiac Disorders ◽

Cellular Components

Autophagy, which is an evolutionarily conserved process according to the lysosomal degradation of cellular components, plays a critical role in maintaining cell homeostasis. Autophagy and mitochondria autophagy (mitophagy) contribute to the preservation of cardiac homeostasis in physiological settings. However, impaired or excessive autophagy is related to a variety of diseases. Recently, a close link between autophagy and cardiac disorders, including myocardial infarction, cardiac hypertrophy, cardiomyopathy, cardiac fibrosis, and heart failure, has been demonstrated. MicroRNAs (miRNAs) are a class of small non-coding RNAs with a length of approximately 21–22 nucleotides (nt), which are distributed widely in viruses, plants, protists, and animals. They function in mediating the post-transcriptional gene silencing. A growing number of studies have demonstrated that miRNAs regulate cardiac autophagy by suppressing the expression of autophagy-related genes in a targeted manner, which are involved in the pathogenesis of heart diseases. This review summarizes the role of microRNAs in cardiac autophagy and related cardiac disorders. Furthermore, we mainly focused on the autophagy regulation pathways, which consisted of miRNAs and their targeted genes.

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A FEM Frontal Impact Study of Square-Section Tubes with Different Structural Solutions for Vehicle Safety

Applied Mechanics and Materials ◽

10.4028/www.scientific.net/amm.798.36 ◽

2015 ◽

Vol 798 ◽

pp. 36-40

Author(s):

Ciro Faria Maia ◽

Guilherme Silame Maranhão Lima ◽

Felipe Grossi L. Amorim ◽

Evandro Queiroz Nunes Vera ◽

Alexander Matioli Pasqual

Keyword(s):

Cross Sections ◽

Initial Velocity ◽

Impact Analysis ◽

Vehicle Safety ◽

Impact Study ◽

Frontal Impact ◽

Structural Differences ◽

Rigid Plane ◽

Structural Solutions

The present paper presents a study of square-section tubes conditioned to a FE dynamic frontal impact analysis, considering a 10.0 m/s initial velocity against an infinitely rigid plane. A 50.0 kg punctual mass is positioned on center of the cross-sections, on the farthest side from the rigid plane and the deceleration pulse is measured along the simulations. After validating the numerical model with analytical solutions, the results are compared for four geometries with little structural differences in order to access the role of each difference on the geometry under crash situations. The results show that adding many triggers to the geometry may not be the best performance solution for crash boxes, since the geometry with few triggers achieved better values of deceleration peak than the others. In addition, the presence of holes showed to be an instability cause to the system. The structural solutions presented could be of great value for future vehicle crash box developments.

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Mutational Analysis of Preamyloid Intermediates: The Role of His-Tyr Interactions in Islet Amyloid Formation

Biophysical Journal ◽

10.1016/j.bpj.2013.12.052 ◽

2014 ◽

Vol 106 (7) ◽

pp. 1520-1527 ◽

Cited By ~ 22

Author(s):

Ling-Hsien Tu ◽

Arnaldo L. Serrano ◽

Martin T. Zanni ◽

Daniel P. Raleigh

Keyword(s):

Mutational Analysis ◽

Amyloid Formation ◽

Islet Amyloid

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Postrecruitment Function of Yeast Med6 Protein during the Transcriptional Activation by Mediator Complex

Biochemistry Research International ◽

10.1155/2018/6406372 ◽

2018 ◽

Vol 2018 ◽

pp. 1-9

Author(s):

Gwang Sik Kim ◽

Young Chul Lee

Keyword(s):

Gene Expression ◽

Reporter Gene ◽

Transcriptional Activation ◽

Reporter Gene Expression ◽

Temperature Sensitive ◽

Internal Deletion ◽

Cell Extracts ◽

Evolutionarily Conserved

Med6 protein (Med6p) is a hallmark component of evolutionarily conserved Mediator complexes, and the genuine role of Med6p in Mediator functions remains elusive. For the functional analysis ofSaccharomyces cerevisiaeMed6p (scMed6p), we generated a series of scMed6p mutants harboring a small internal deletion. Genetic analysis of these mutants revealed that three regions (amino acids 33–42 (Δ2), 125–134 (Δ5), and 157–166 (Δ6)) of scMed6p are required for cell viability and are located at highly conserved regions of Med6 homologs. Notably, the Med6p-Δ2 mutant was barely detectable in whole-cell extracts and purified Mediator, suggesting a loss of Mediator association and concurrent rapid degradation. Consistent with this, the recombinant forms of Med6p having these mutations partially (Δ2) restore or fail (Δ5 and Δ6) to restore in vitro transcriptional defects caused by temperature-sensitivemed6mutation. In an artificial recruitment assay, Mediator containing a LexA-fused wild-type Med6p or Med6p-Δ5 was recruited to thelexAoperator region with TBP and activated reporter gene expression. However, the recruitment of Mediator containing LexA-Med6p-Δ6 tolexAoperator region resulted in neither TBP recruitment nor reporter gene expression. This result demonstrates a pivotal role of Med6p in the postrecruitment function of Mediator, which is essential for transcriptional activation by Mediator.

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WDR31 is a novel ciliopathy protein displaying functional redundancy with GTPase-activating proteins ELMOD and RP2 in recruiting BBSome to cilium

10.21203/rs.3.rs-622797/v1 ◽

2021 ◽

Author(s):

Sebiha Cevik ◽

Lama Alabdi ◽

Xiaoyu Peng ◽

Tina Beyer ◽

Atiyye Zorluer ◽

...

Keyword(s):

Clinical Features ◽

Renal Agenesis ◽

Rare Disorders ◽

Compartment Analysis ◽

C Elegans ◽

Gtpase Activating Proteins ◽

Mechanistic Analysis ◽

Evolutionarily Conserved ◽

Null Mutants

Abstract The term “ciliopathy” refers to a group of over 35 rare disorders characterized by defective cilia and many overlapping clinical features, such as hydrocephalus, cerebellar vermis hypoplasia, polydactyly, and retinopathy. Even though many genes have been implicated in ciliopathies, the genetic pathogenesis in certain cases remains still undisclosed. Here, we identified a homozygous truncating variant in WDR31 in a patient with a typical ciliopathy phenotype encompassing congenital hydrocephalus, polydactyly, and renal agenesis. WDR31 is an evolutionarily conserved protein that localizes to the cilium and cilia-related compartment. Analysis from zebrafish supports the role of WDR31 in regulating the cilia morphology. The CRISPR/Cas9 knock-in (p.Arg261del) C. elegans model of the patient variant (p.Arg268*) reproduced several cilia-related defects observed in wdr-31 null mutants. Mechanistic analysis from C. elegans revealed that WDR-31 functions redundantly with ELDM-1 (ELMOD protein) and RPI-2 (RP2) to regulate the IFT trafficking through controlling the cilia entry of the BBSome. This work revealed WDR31 as a new ciliopathy protein that regulates IFT and BBSome trafficking.

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Mutational Analysis of a Wheat O-methyltransferase Involved in Flavonoid Metabolism

Plants ◽

10.3390/plants11020164 ◽

2022 ◽

Vol 11 (2) ◽

pp. 164

Author(s):

Alexander B. Cain ◽

Shu Yu ◽

Li Tian

Keyword(s):

Mutational Analysis ◽

Tetraploid Wheat ◽

Hydroxyl Groups ◽

Loss Of Function ◽

Soluble Phenolics ◽

Mutant Lines ◽

Similar Growth ◽

Close Homolog ◽

Lignin Deposition

Methylated flavones, and tricin in particular, have been implicated in protecting wheat plants against a variety of biotic and abiotic stresses. Methylated flavones are produced via O-methylation of the hydroxyl groups in flavones, which is catalyzed by O-methyltransferases (OMTs). To examine the role of wheat OMT2 in methylated flavone biosynthesis and facilitate interrogation of tricin functions in wheat-environment interactions, loss-of-function mutants of OMT2 homoeologs, omt-A2 and omt-B2, were identified from a tetraploid wheat Targeting Induced Local Lesions in Genomes (TILLING) mutant population and crossed to generate the omt-A2omt-B2 double mutant. Although tricin and most other soluble phenolics did not differ in leaves and glumes of TILLING control and the omt-A2, omt-B2, and omt-A2 omt-B2 mutants, chlorogenic acid was increased in glumes of omt-A2 omt-B2 relative to TILLING control, suggesting that it might serve as a substrate for OMT2. The omt2 mutant lines showed similar growth phenotypes as well as comparable lignin deposition in cell walls of stems compared to TILLING control. These results collectively suggest that OMT2 and its close homolog OMT1 may possess overlapping activities in tricin production, with OMT1 compensating for the missing OMT2 activities in the omt2 mutant lines.

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Insights into biological functions across species: examining the role of Rab proteins in YIP1 family function

Biochemical Society Transactions ◽

10.1042/bst0330614 ◽

2005 ◽

Vol 33 (4) ◽

pp. 614-618 ◽

Cited By ~ 6

Author(s):

C.Z. Chen ◽

R.N. Collins

Keyword(s):

Membrane Proteins ◽

Protein Function ◽

Evolutionary Conservation ◽

Biological Role ◽

Rab Proteins ◽

Biological Functions ◽

Human Homologue ◽

Family Function ◽

Evolutionarily Conserved

The YIP1 family comprises an evolutionarily conserved group of membrane proteins, which share the ability to bind di-prenylated Rab proteins. The biochemical capability of YIP1 family proteins suggests a possible role in the cycle of physical localization of Rab proteins between their cognate membranes and the cytosol. YIP1 is essential for viability in yeast and a deletion of YIP1 can be rescued with the human homologue YIP1A. We have made use of this evolutionary conservation of function to generate a series of mutant alleles of YIP1 to investigate the biological role of Yip1p. Our findings indicate evidence for the participation of Yip1p in both Rab and COPII protein function; at present, we are not able to distinguish between the models that these roles represent, i.e. independent or dependent activities of Yip1p.

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Spalt modifies EGFR-mediated induction of chordotonal precursors in the embryonic PNS of Drosophila promoting the development of oenocytes

Development ◽

10.1242/dev.128.5.711 ◽

2001 ◽

Vol 128 (5) ◽

pp. 711-722 ◽

Cited By ~ 3

Author(s):

T.E. Rusten ◽

R. Cantera ◽

J. Urban ◽

G. Technau ◽

F.C. Kafatos ◽

...

Keyword(s):

Nervous System ◽

Cell Fate ◽

System Development ◽

Cell Types ◽

Nervous System Development ◽

Dual Function ◽

Evolutionarily Conserved ◽

A Cell ◽

And Migration

Genes of the spalt family encode nuclear zinc finger proteins. In Drosophila melanogaster, they are necessary for the establishment of head/trunk identity, correct tracheal migration and patterning of the wing imaginal disc. Spalt proteins display a predominant pattern of expression in the nervous system, not only in Drosophila but also in species of fish, mouse, frog and human, suggesting an evolutionarily conserved role for these proteins in nervous system development. Here we show that Spalt works as a cell fate switch between two EGFR-induced cell types, the oenocytes and the precursors of the pentascolopodial organ in the embryonic peripheral nervous system. We show that removal of spalt increases the number of scolopodia, as a result of extra secondary recruitment of precursor cells at the expense of the oenocytes. In addition, the absence of spalt causes defects in the normal migration of the pentascolopodial organ. The dual function of spalt in the development of this organ, recruitment of precursors and migration, is reminiscent of its role in tracheal formation and of the role of a spalt homologue, sem-4, in the Caenorhabditis elegans nervous system.

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