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Gopinathan L.,Institute of Molecular and Cell Biology IMCB | Ratnacaram C.K.,Institute of Molecular and Cell Biology IMCB | Kaldis P.,Institute of Molecular and Cell Biology IMCB | Kaldis P.,National University of Singapore
Results and Problems in Cell Differentiation | Year: 2011

The identification of new members in the Cdk and cyclin families, functions for many of which are still emerging, has added new facets to the cell cycle regulatory network. With roles extending beyond the classical regulation of cell cycle progression, these new players are involved in diverse processes such as transcription, neuronal function, and ion transport. Members closely related to Cdks and cyclins such as the Speedy/RINGO proteins offer fresh insights and hope for filling in the missing gaps in our understanding of cell division. This chapter will present a broad outlook on the cell cycle and its key regulators with special emphasis on the less-studied members and their emerging roles. © 2011 Springer-Verlag Berlin Heidelberg.


Cildir G.,Institute of Molecular and Cell Biology IMCB | Cildir G.,National University of Singapore | Akincilar S.C.,Institute of Molecular and Cell Biology IMCB | Akincilar S.C.,National University of Singapore | And 2 more authors.
Trends in Molecular Medicine | Year: 2013

Inflammation is indispensable for host homeostasis against invading pathogens and efficient wound healing upon tissue malfunction and has to be tightly controlled by various mechanisms to limit excess responses harmful to host tissues. A myriad of disease conditions ranging from type 2 diabetes (T2D) to neurodegenerative and cardiovascular disorders are now shown to progress due to persistent, unresolved inflammation in metabolic tissues such as adipose, liver, pancreas, muscle, and brain. However, their underlying mechanisms are incompletely understood. The actions of innate and adaptive immune cells in these ailments are increasingly appreciated so much so that a new research area called 'immunometabolism' has emerged. In this review, we will highlight the fundamental roles of various immune cells in adipose tissue during the initiation and progression of obesity-induced inflammation and discuss potential anti-inflammatory therapies from different mechanistic points of view. © 2013 Elsevier Ltd.


Vaisman A.,U.S. National Institutes of Health | McDonald J.P.,U.S. National Institutes of Health | Huston D.,U.S. National Institutes of Health | Kuban W.,U.S. National Institutes of Health | And 4 more authors.
PLoS Genetics | Year: 2013

Stringent steric exclusion mechanisms limit the misincorporation of ribonucleotides by high-fidelity DNA polymerases into genomic DNA. In contrast, low-fidelity Escherichia coli DNA polymerase V (pol V) has relatively poor sugar discrimination and frequently misincorporates ribonucleotides. Substitution of a steric gate tyrosine residue with alanine (umuC_Y11A) reduces sugar selectivity further and allows pol V to readily misincorporate ribonucleotides as easily as deoxynucleotides, whilst leaving its poor base-substitution fidelity essentially unchanged. However, the mutability of cells expressing the steric gate pol V mutant is very low due to efficient repair mechanisms that are triggered by the misincorporated rNMPs. Comparison of the mutation frequency between strains expressing wild-type and mutant pol V therefore allows us to identify pathways specifically directed at ribonucleotide excision repair (RER). We previously demonstrated that rNMPs incorporated by umuC_Y11A are efficiently removed from DNA in a repair pathway initiated by RNase HII. Using the same approach, we show here that mismatch repair and base excision repair play minimal back-up roles in RER in vivo. In contrast, in the absence of functional RNase HII, umuC_Y11A-dependent mutagenesis increases significantly in ΔuvrA, uvrB5 and ΔuvrC strains, suggesting that rNMPs misincorporated into DNA are actively repaired by nucleotide excision repair (NER) in vivo. Participation of NER in RER was confirmed by reconstituting ribonucleotide-dependent NER in vitro. We show that UvrABC nuclease-catalyzed incisions are readily made on DNA templates containing one, two, or five rNMPs and that the reactions are stimulated by the presence of mispaired bases. Similar to NER of DNA lesions, excision of rNMPs proceeds through dual incisions made at the 8th phosphodiester bond 5′ and 4th-5th phosphodiester bonds 3′ of the ribonucleotide. Ribonucleotides misinserted into DNA can therefore be added to the broad list of helix-distorting modifications that are substrates for NER.


Goh L.L.,Singapore Institute of Medical Biology | Ed M.,Singapore Institute of Medical Biology | Ed M.,Institute of Molecular and Cell Biology IMCB
PLoS ONE | Year: 2010

Background: Rnd3 (RhoE) protein belongs to the unique branch of Rho family GTPases that has low intrinsic GTPase activity and consequently remains constitutively active [1,2]. The current consensus is that Rnd1 and Rnd3 function as important antagonists of RhoA signaling primarily by activating the ubiquitous p190 RhoGAP [3], but not by inhibiting the ROCK family kinases. Methodology/Principal Findings: Rnd3 is abundant in mouse embryonic stem (mES) cells and in an unbiased two-step affinity purification screen we identified a new Rnd3 target, termed synectin-binding RhoA exchange factor (Syx), by mass spectrometry. The Syx interaction with Rnd3 does not occur through the Syx DH domain but utilizes a region similar to the classic Raf1 Ras-binding domain (RBD), and most closely related to those in RGS12 and RGS14. We show that Syx behaves as a genuine effector of Rnd3 (and perhaps Rnd1), with binding characteristics similar to p190-RhoGAP. Morpholinooligonucleotide knockdown of Syx in zebrafish at the one cell stage resulted in embryos with shortened anterior-posterior body axis: this phenotype was effectively rescued by introducing mouse Syx1b mRNA. A Rnd3-binding defective mutant of Syx1b mutated in the RBD (E164A/R165D) was more potent in rescuing the embryonic defects than wild-type Syx1b, showing that Rnd3 negatively regulates Syx activity in vivo. Conclusions/Significance: This study uncovers a well defined Rnd3 effector Syx which is widely expressed and directly impacts RhoA activation. Experiments conducted in vivo indicate that Rnd3 negatively regulates Syx, and that as a RhoA-GEF it plays a key role in early embryonic cell shape changes. Thus a connection to signaling via the planar cell polarity pathway is suggested. © 2010 Goh, Manser.


Adon A.M.,Emory University | Zeng X.,Emory University | Harrison M.K.,Emory University | Sannem S.,Emory University | And 3 more authors.
Molecular and Cellular Biology | Year: 2010

The two mitotic centrosomes direct spindle bipolarity to maintain euploidy. Centrosome amplification - the acquisition of ≥3 centrosomes - generates multipolar mitoses, aneuploidy, and chromosome instability to promote cancer biogenesis. While much evidence suggests that Cdk2 is the major conductor of the centrosome cycle and that it mediates centrosome amplification induced by various altered tumor suppressors, the role played by Cdk4 in a normal or deregulated centrosome cycle is unknown. Using a gene knockout approach, we report that Cdk2 and Cdk4 are critical to the centrosome cycle, since centrosome separation and duplication are premature in Cdk2-/- mouse embryonic fibroblasts (MEFs) and are compromised in Cdk4-/- MEFs. Additionally, ablation of Cdk4 or Cdk2 abrogates centrosome amplification and chromosome instability in p53-null MEFs. Absence of Cdk2 or Cdk4 prevents centrosome amplification by abrogating excessive centriole duplication. Furthermore, hyperactive Cdk2 and Cdk4 deregulate the licensing of the centrosome duplication cycle in p53-null cells by hyperphosphorylating nucleophosmin (NPM) at Thr199, as evidenced by observations that ablation of Cdk2, Cdk4, or both Cdk2 and Cdk4 abrogates that excessive phosphorylation. Since a mutant form of NPM lacking the G1 Cdk phosphorylation site (NPMT199A) prevents centrosome amplification to the same extent as ablation of Cdk2 or Cdk4, we conclude that the Cdk2/Cdk4/NPM pathway is a major guardian of centrosome dysfunction and genomic integrity. Copyright © 2010, American Society for Microbiology. All Rights Reserved.


Ingham P.W.,Institute of Molecular and Cell Biology IMCB
Genes and Development | Year: 2012

Inspired by a zebrafish mutation, two recent studies by Creanga and colleagues (pp. 1312-1325) and Tukachinsky and colleagues have shed new light on the way in which lipidated Hedgehog proteins are secreted and released from expressing cells, suggesting a model for the sequential action of the Disp and Scube2 proteins in this process. © 2012 by Cold Spring Harbor Laboratory Press.


Gill D.J.,Institute of Molecular and Cell Biology IMCB | Clausen H.,Copenhagen University | Bard F.,Institute of Molecular and Cell Biology IMCB
Trends in Cell Biology | Year: 2011

O-GalNAc glycosylation of proteins confers essential structural, protective and signaling roles in eumetazoans. Addition of O-glycans onto proteins is an extremely complex process that regulates both sites of attachment and the types of oligosaccharides added. Twenty distinct polypeptide GalNAc-transferases (GalNAc-Ts) initiate O-glycosylation and fine-tuning their expression provides a mechanism for regulating this action. Recently, a new mode of regulation has emerged where activation of Src kinase selectively redistributes Golgi-localized GalNAc-Ts to the ER. This relocalization results in a strong increase in the density of O-glycan decoration. In this review, we discuss how different mechanisms can regulate the number and the types of O-glycans decorating proteins. In addition, we speculate how Src-dependent relocation of GalNAc-Ts could play an important role in cancerous cellular transformation. © 2010 Elsevier Ltd.


Cheow L.F.,Microfluidics | Quake S.R.,Microfluidics | Quake S.R.,Howard Hughes Medical Institute | Burkholder W.F.,Microfluidics | Messerschmidt D.M.,Institute of Molecular and Cell Biology IMCB
Nature Protocols | Year: 2015

This protocol details a method for measuring the DNA methylation state of multiple target sites in single cells, otherwise known as single-cell restriction analysis of methylation (SCRAM). The basic steps include isolating and lysing single cells, digesting genomic DNA with a methylation-sensitive restriction endonuclease (MSRE) and amplification of multiple targets by two rounds of PCR to determine the methylation status of target sites. The method can reliably and accurately detect the methylation status of multiple target sites in each single cell, and it can be completed in a relatively short time (<2 d) at low cost. Consequently, the method may be preferable over whole-genome methods in applications requiring highly reliable and cost-effective coverage of specific target sites in all cells from a sample and in cases when the DNA methylation states of single CpG sites are representative of the methylation status of corresponding regions of interest. © 2015 Nature America, Inc.


Migliori V.,Institute of Molecular and Cell Biology IMCB | Phalke S.,Institute of Molecular and Cell Biology IMCB | Bezzi M.,Institute of Molecular and Cell Biology IMCB | Guccione E.,Institute of Molecular and Cell Biology IMCB
Epigenomics | Year: 2010

Post-translational modifications (PTMs) are commonly used to modify protein function. Modifications such as phosphorylation, acetylation and methylation can influence the conformation of the modified protein and its interaction with other proteins or DNA. In the case of histones, PTMs on specific residues can influence chromatin structure and function by modifying the biochemical properties of key amino acids. Histone methylation events, especially on arginine- and lysine-residues, are among the best-characterized PTMs, and many of these modifications have been linked to downstream effects. The addition of a methyl group to either residue results in a slight increase in hydrophobicity, in the loss of a potential hydrogen-bond donor site and, in the alteration of the protein interaction surface. Thus far, a number of protein domains have been demonstrated to directly bind to methylated lysine residues. However, the biochemical mechanisms linking histone arginine methylation to downstream biological outputs remain poorly characterized. This review will focus on the role of histone arginine methylation in transcriptional regulation and on the crosstalk between arginine methylation and other PTMs. We will discuss the mechanisms by which differentially methylated arginines on histones modulate transcriptional outcomes and contribute to the complexity of the 'histone code. © 2010 Future Medicine Ltd.


Tay H.G.,Singapore Institute of Medical Biology | Ng Y.W.,Institute of Molecular and Cell Biology IMCB | Manser E.,Singapore Institute of Medical Biology | Manser E.,Institute of Molecular and Cell Biology IMCB
PLoS ONE | Year: 2010

Background: In early vertebrate development, embryonic tissues modulate cell adhesiveness and acto-myosin contractility to correctly orchestrate the complex processes of gastrulation. E-cadherin (E-cadh) is the earliest expressed cadherin and is needed in the mesendodermal progenitors for efficient migration [1,2]. Regulatory mechanisms involving directed E-cadh trafficking have been invoked downstream of Wnt11/5 signaling [3]. This non-canonical Wnt pathway regulates RhoA-ROK/ DAAM1 to control the acto-myosin network. However, in this context nothing is known of the intracellular signals that participate in the correct localization of E-cadh, other than a need for Rab5c signaling [3]. Methodology/Principal Findings: By studying loss of Chp induced by morpholino-oligonucleotide injection in zebrafish, we find that the vertebrate atypical Rho-GTPase Chp is essential for the proper disposition of cells in the early embryo. The underlying defect is not leading edge F-actin assembly (prominent in the cells of the envelope layer), but rather the failure to localize E-cadh and β-catenin at the adherens junctions. Loss of Chp results in delayed epiboly that can be rescued by mRNA co-injection, and phenocopies zebrafish E-cadh mutants [4,5]. This new signaling pathway involves activation of an effector kinase PAK, and involvement of the adaptor PAK-interacting exchange factor PIX. Loss of signaling by any of the three components results in similar underlying defects, which is most prominent in the epithelial-like envelope layer. Conclusions/Significance: Our current study uncovers a developmental pathway involving Chp/PAK/PIX signaling, which helps co-ordinate E-cadh disposition to promote proper cell adhesiveness, and coordinate movements of the three major cell layers in epiboly. Our data shows that without Chp signaling, E-cadh shifts to intracellular vesicles rather than the adhesive contacts needed for directed cell movement. These events may mirror the requirement for PAK2 signaling essential for the proper formation of the blood-brain barrier [6,7].© 2010 Tay et al.

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