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1.  Spatiotemporal Regulation of the Anaphase-Promoting Complex in Mitosis 
The appropriate timing of events that lead to chromosome segregation during mitosis and cytokinesis is essential to prevent aneuploidy, and defects in these processes can contribute to tumorigenesis. Key mitotic regulators are controlled through ubiquitylation and proteasome-mediated degradation. The Anaphase-Promoting Complex or Cyclosome (APC/C) is an E3 ubiquitin ligase that has a crucial function in the regulation of the mitotic cell cycle, particularly at the onset of anaphase and during mitotic exit. Co-activator proteins, inhibitor proteins, protein kinases and phosphatases interact with the APC/C to temporally and spatially control its activity and thus ensure accurate timing of mitotic events.
doi:10.1038/nrm3934
PMCID: PMC4386896  PMID: 25604195
2.  Mechanisms guiding primordial germ cell migration: strategies from different organisms 
Preface
The regulated migration of cells is essential for development and tissue homeostasis, and aberrant cell migration can lead to an impaired immune response and the progression of cancer. Primordial germ cells (PGCs), precursors to sperm and eggs, have to migrate across the embryo to reach somatic gonadal precursors (SGPs) and fulfill their function. Studies of model organisms have revealed that, despite important differences, several features of PGC migration are conserved. PGCs require both an intrinsic motility program and external guidance cues to survive and successfully migrate. Proper guidance involves both attractive and repulsive cues mediated by protein and lipid signalling.
doi:10.1038/nrm2815
PMCID: PMC4521894  PMID: 20027186
3.  Mechanotransduction and extracellular matrix homeostasis 
Preface
Soft connective tissues at steady state are yet dynamic; resident cells continually read environmental cues and respond to promote homeostasis, including maintenance of the mechanical properties of the extracellular matrix that are fundamental to cellular and tissue health. The mechanosensing process involves assessment of the mechanics of the matrix by the cells through integrins and the actomyosin cytoskeleton, and is followed by a mechano-regulation process that includes the deposition, rearrangement, or removal of matrix to maintain overall form and function. Progress toward understanding the molecular, cellular, and tissue scale effects that promote mechanical homeostasis has helped identify key questions for future research.
doi:10.1038/nrm3896
PMCID: PMC4513363  PMID: 25355505
mechanosensing; mechanoregulation; integrins; actomyosin; extracellular matrix
4.  Diversity and selectivity in mRNA translation on the endoplasmic reticulum 
Pioneering electron microscopy studies defined two primary populations of ribosomes in eukaryotic cells: one freely dispersed through the cytoplasm and the other bound to the surface of the endoplasmic reticulum (ER). Subsequent investigations revealed a specialized function for each population, with secretory and integral membrane protein-encoding mRNAs translated on ER-bound ribosomes, and cytosolic protein synthesis was widely attributed to free ribosomes. Recent findings have challenged this view, and transcriptome-scale studies of mRNA distribution and translation have now demonstrated that ER-bound ribosomes also function in the translation of a large fraction of mRNAs that encode cytosolic proteins. These studies suggest a far more expansive role for the ER in transcriptome expression, where membrane and secretory protein synthesis represents one element of a multifaceted and dynamic contribution to post-transcriptional gene expression.
doi:10.1038/nrm3958
PMCID: PMC4494666  PMID: 25735911
5.  When pathways collide: collaboration and connivance among signaling proteins in development 
Signal transduction pathways interact at various levels in defining tissue morphology, size and differentiation during development. Understanding of the mechanisms by which these pathways collude has been greatly enhanced by recent insights into how shared components are independently regulated and how the activity of one system is contextualized by others. Traditionally, the components of signalling pathways have been assumed to show pathway fidelity and to act with a high degree of autonomy. However, as illustrated by the Wnt and Hippo pathways, there is increasing evidence that components are often shared between multiple pathways and other components talk to each other through multiple mechanisms.
doi:10.1038/nrm2902
PMCID: PMC4489880  PMID: 20461097 CAMSID: cams1564
6.  Intrinsically Disordered Proteins in Cellular Signaling and Regulation 
Intrinsically disordered proteins (IDPs) are important components of the cellular signaling machinery, allowing the same polypeptide to undertake different interactions with different consequences. IDPs are subject to combinatorial post-translational modifications and alternative splicing, adding complexity to regulatory networks and providing a mechanism for tissue-specific signaling. IDPs participate in assembly of signaling complexes and in the dynamic self-assembly of membrane-less nuclear and cytoplasmic organelles. Experimental, computational and bioinformatic analysis combine to identify and characterize disordered regions of proteins, leading to a greater appreciation of their widespread role in biological processes.
doi:10.1038/nrm3920
PMCID: PMC4405151  PMID: 25531225
7.  In the right place at the right time: visualizing and understanding mRNA localization 
The spatial regulation of protein translation is an efficient way to create functional and structural asymmetries in cells. Recent research has furthered our understanding of how individual cells spatially organize protein synthesis, by applying innovative technology to characterize the relationship between mRNAs and their regulatory proteins, single-mRNA trafficking dynamics, physiological effects of abrogating mRNA localization in vivo and for endogenous mRNA labelling. The implementation of new imaging technologies has yielded valuable information on mRNA localization, for example, by observing single molecules in tissues. The emerging movements and localization patterns of mRNAs in morphologically distinct unicellular organisms and in neurons have illuminated shared and specialized mechanisms of mRNA localization, and this information is complemented by transgenic and biochemical techniques that reveal the biological consequences of mRNA mislocalization.
doi:10.1038/nrm3918
PMCID: PMC4484810  PMID: 25549890
8.  THE MECHANISM OF EUKARYOTIC TRANSLATION INITIATION AND PRINCIPLES OF ITS REGULATION 
PREFACE
Protein synthesis is principally regulated at the initiation stage (rather than during elongation or termination), allowing rapid, reversible and spatial control over gene expression. Progress over recent years in determining the structures and activities of initiation factors, and in mapping their interactions within ribosomal initiation complexes, has significantly advanced our understanding of the complex translation initiation process. These developments have provided a solid foundation for studies of regulation of initiation by mechanisms that include modulation of the activity of initiation factors (which affects almost all scanning-dependent initiation), or via sequence-specific RNA-binding proteins and microRNAs (which thus impact individual mRNAs).
doi:10.1038/nrm2838
PMCID: PMC4461372  PMID: 20094052
9.  The structure, function and evolution of proteins that bind DNA and RNA 
Proteins that bind both DNA and RNA epitomize the ability to perform multiple functions by a single gene product. Such DNA- and RNA-binding proteins (DRBPs) regulate many cellular processes, including transcription, translation, gene silencing, microRNA biogenesis and telomere maintenance. Proteins that bind RNA were typically considered as functionally distinct from proteins that bind DNA and studied independently. This practice is becoming outdated, in part due to the discovery of long non-coding RNAs (lncRNAs) that target DNA-binding proteins. DRBPs have unique functional characteristics that stem from their specific structural attributes; these have evolved early in evolution and are widely conserved.
doi:10.1038/nrm3884
PMCID: PMC4280011  PMID: 25269475
10.  Signaling dynamics in the spindle checkpoint response 
doi:10.1038/nrm3888
PMCID: PMC4283840  PMID: 25303117
11.  Molecular basis of physiological heart growth: fundamental concepts and new players 
The heart hypertrophies in response to developmental signals as well as increased workload. Although adult-onset hypertrophy can ultimately lead to disease, cardiac hypertrophy is not necessarily maladaptive and can even be beneficial. Progress has been made in our understanding of the structural and molecular characteristics of physiological cardiac hypertrophy, as well as of the endocrine effectors and associated signalling pathways that regulate it. Physiological hypertrophy is initiated by finite signals, which include growth hormones (such as thyroid hormone, insulin, insulin-like growth factor 1 and vascular endothelial growth factor) and mechanical forces that converge on a limited number of intracellular signalling pathways (such as PI3K, AKT, AMP-activated protein kinase and mTOR) to affect gene transcription, protein translation and metabolism. Harnessing adaptive signalling mediators to reinvigorate the diseased heart could have important medical ramifications.
doi:10.1038/nrm3495
PMCID: PMC4416212  PMID: 23258295
12.  The dynamic epitranscriptome: N6-methyladenosine and gene expression control 
N6-methyladenosine (m6A) is a modified base that has long been known to be present in noncoding RNAs, ribosomal RNA, polyadenylated RNA and at least one mammalian mRNA. However, our understanding of the prevalence of this modification has been fundamentally redefined by transcriptome-wide m6A mapping studies, which have shown that m6A is present in a large subset of the transcriptome in specific regions of mRNA. This suggests that mRNA may undergo post-transcriptional methylation to regulate its fate and function, analogous to methyl modifications in DNA. Thus, the pattern of methylation constitutes an mRNA ‘epitranscriptome’. The identification of adenosine methyltransferases (‘writers’), m6A demethylating enzymes (‘erasers’) and m6A binding proteins (‘readers’) is helping to define cellular pathways for the post-transcriptional regulation of mRNAs.
doi:10.1038/nrm3785
PMCID: PMC4393108  PMID: 24713629
13.  Signals for the lysosome: a control center for cellular clearance and energy metabolism 
Preface
For a long time lysosomes were considered merely to be cellular “incinerators” involved in the degradation and recycling of cellular waste. However, there is now compelling evidence indicating that lysosomes have a much broader function and that they are involved in fundamental processes such as secretion, plasma membrane repair, signaling and energy metabolism. Furthermore, the essential role of lysosomes in the autophagic pathway puts these organelles at the crossroads of several cellular processes, with significant implications for health and disease. The identification of a master gene, transcription factor EB (TFEB), that regulates lysosomal biogenesis and autophagy, has revealed how the lysosome adapts to environmental cues, such as starvation, and suggests novel therapeutic strategies for modulating lysosomal function in human disease.
doi:10.1038/nrm3565
PMCID: PMC4387238  PMID: 23609508
14.  Regulated protein turnover: snapshots of the proteasome in action 
The ubiquitin-proteasome system (UPS) is the main ATP-dependent protein degradation pathway in the cytosol and nucleus of eukaryotic cells. At its centre is the 26S proteasome, which degrades regulatory proteins and mis-folded or damaged proteins. In a major breakthrough, several groups have determined high-resolution structures of the entire 26S proteasome particle in different nucleotide conditions and with and without substrate using cryo-electron microscopy combined with other techniques. These structures bring some surprising insights into the functional mechanism of the proteasome and will provide invaluable guidance for genetic and biochemical studies of this key regulatory system.
doi:10.1038/nrm3741
PMCID: PMC4384331  PMID: 24452470
15.  Mitochondrial dynamics and inheritance during cell division, development and disease 
Preface
During cell division, it is critical to properly partition functional sets of organelles to each daughter cell. The partitioning of mitochondria shares some common features with other organelles, particularly in their interactions with cytoskeletal elements to facilitate delivery to the daughter cells. However, mitochondria have unique features – including their own genome and a maternal mode of germline transmission – that place additional demands on this process. We discuss the mechanisms regulating mitochondrial segregation during cell division, oogenesis, fertilization and tissue development. The mechanisms that ensure the integrity of these organelles and their DNA include fusion-fission dynamics, organelle transport, mitophagy, and genetic selection of functional genomes. Defects in these processes can lead to cell and tissue pathologies.
doi:10.1038/nrm3877
PMCID: PMC4250044  PMID: 25237825
16.  Three-dimensional organotypic culture: experimental models of mammalian biology and disease 
Mammalian organs are challenging to study as they are fairly inaccessible to experimental manipulation and optical observation. Recent advances in three-dimensional (3D) culture techniques, coupled with the ability to independently manipulate genetic and microenvironmental factors, have enabled the real-time study of mammalian tissues. These systems have been used to visualize the cellular basis of epithelial morphogenesis, to test the roles of specific genes in regulating cell behaviours within epithelial tissues and to elucidate the contribution of microenvironmental factors to normal and disease processes. Collectively, these novel models can be used to answer fundamental biological questions and generate replacement human tissues, and they enable testing of novel therapeutic approaches, often using patient-derived cells.
doi:10.1038/nrm3873
PMCID: PMC4352326  PMID: 25237826
17.  All tangled up: how cells direct, manage and exploit topoisomerase function 
Preface
Topoisomerases are complex molecular machines that modulate DNA topology to maintain chromosome superstructure and integrity. Although capable of stand-alone activity in vitro, topoisomerases frequently are linked to larger pathways and systems that resolve specific DNA superstructures and intermediates arising from cellular processes such as DNA repair, transcription, replication, and chromosome compaction. Topoisomerase activity is indispensible to cells, but requires the transient breakage of DNA strands. This property has been exploited, often for significant clinical benefit, by various exogenous agents that interfere with cell proliferation. Despite decades of study, surprising findings involving topoisomerases continue to emerge with respect to their cellular function, regulation, and utility as therapeutic targets.
doi:10.1038/nrm3228
PMCID: PMC4351964  PMID: 22108601
Topoisomerase; DNA replication; DNA repair; transcription; chromosome structure; topology; drug discovery
18.  RNAi screening comes of age: improved techniques and complementary approaches 
Gene silencing through sequence-specific targeting of mRNAs by RNAi has enabled genome-wide functional screens in cultured cells and in vivo in model organisms. These screens have resulted in the identification of new cellular pathways and potential drug targets. Considerable progress has been made to improve the quality of RNAi screen data through the development of new experimental and bioinformatics approaches. The recent availability of genome-editing strategies, such as the CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 system, when combined with RNAi, could lead to further improvements in screen data quality and follow-up experiments, thus promoting our understanding of gene function and gene regulatory networks.
doi:10.1038/nrm3860
PMCID: PMC4204798  PMID: 25145850
19.  Chaperone machines for protein folding, unfolding and disaggregation 
Molecular chaperones are diverse families of multidomain proteins that have evolved to assist nascent proteins to reach their native fold, protect subunits from heat shock during the assembly of complexes, prevent protein aggregation or mediate targeted unfolding and disassembly. Their increased expression in response to stress is a key factor in the health of the cell and longevity of an organism. Unlike enzymes with their precise and finely tuned active sites, chaperones are heavy-duty molecular machines that operate on a wide range of substrates. The structural basis of their mechanism of action is being unravelled (in particular for the heat shock proteins HSP60, HSP70, HSP90 and HSP100) and typically involves massive displacements of 20–30 kDa domains over distances of 20–50 Å and rotations of up to 100°.
doi:10.1038/nrm3658
PMCID: PMC4340576  PMID: 24026055
20.  CREB and the CRTC co-activators: sensors for hormonal and metabolic signals 
The cyclic AMP-responsive element-binding protein (CREB) is phosphorylated in response to a wide variety of signals, yet target gene transcription is only increased in a subset of cases. Recent studies indicate that CREB functions in concert with a family of latent cytoplasmic co-activators called cAMP-regulated transcriptional co-activators (CRTCs), which are activated through dephosphorylation. A dual requirement for CREB phosphorylation and CRTC dephosphorylation is likely to explain how these activator–co-activator cognates discriminate between different stimuli. Following their activation, CREB and CRTCs mediate the effects of fasting and feeding signals on the expression of metabolic programmes in insulin-sensitive tissues.
doi:10.1038/nrm3072
PMCID: PMC4324555  PMID: 21346730
21.  Remodelling the extracellular matrix in development and disease 
The extracellular matrix (ECM) is a highly dynamic structure that is present in all tissues and continuously undergoes controlled remodelling. This process involves quantitative and qualitative changes in the ECM, mediated by specific enzymes that are responsible for ECM degradation, such as metalloproteinases. The ECM interacts with cells to regulate diverse functions, including proliferation, migration and differentiation. ECM remodelling is crucial for regulating the morphogenesis of the intestine and lungs, as well as of the mammary and submandibular glands. Dysregulation of ECM composition, structure, stiffness and abundance contributes to several pathological conditions, such as fibrosis and invasive cancer. A better understanding of how the ECM regulates organ structure and function and of how ECM remodelling affects disease progression will contribute to the development of new therapeutics.
doi:10.1038/nrm3904
PMCID: PMC4316204  PMID: 25415508
22.  [No title available] 
PMCID: PMC4060434  PMID: 24452469
23.  Illuminating cell signalling with optogenetic tools 
The light-based control of ion channels has been transformative for the neurosciences, but the optogenetic toolkit does not stop there. An expanding number of proteins and cellular functions have been shown to be controlled by light, and the practical considerations in deciding between reversible optogenetic systems (such as systems that use light-oxygen-voltage domains, phytochrome proteins, cryptochrome proteins and the fluorescent protein Dronpa) are well defined. The field is moving beyond proof of concept to answering real biological questions, such as how cell signalling is regulated in space and time, that were difficult or impossible to address with previous tools.
doi:10.1038/nrm3837
PMCID: PMC4145075  PMID: 25027655
24.  Capping Protein Regulators Fine-Tune Actin Assembly Dynamics 
Capping protein (CP) regulates actin polymerization by binding the barbed end of an actin filament, which blocks addition and loss of actin subunits. Recent structural and biochemical studies provide new insight into how cells control the actin capping activity of CP. Several molecules indirectly regulate CP by interacting with filament barbed ends and preventing binding of CP; others bind directly to CP and sterically block its interaction with an actin filament. A diverse and otherwise unrelated set of proteins contains a motif for CP regulation termed the “Capping Protein Interaction” (CPI) motif. These proteins bind directly to CP, recruit or target CP to a subcellular location, and modulate its actin-capping activity via allosteric effects.
doi:10.1038/nrm3869
PMCID: PMC4271544  PMID: 25207437
25.  Molecular mechanisms of epithelial–mesenchymal transition 
The transdifferentiation of epithelial cells into motile mesenchymal cells, a process known as epithelial–mesenchymal transition (EMT), is integral in development, wound healing and stem cell behaviour, and contributes pathologically to fibrosis and cancer progression. This switch in cell differentiation and behaviour is mediated by key transcription factors, including SNAIL, zinc-finger E-box-binding (ZEB) and basic helix-loop-helix transcription factors, the functions of which are finely regulated at the transcriptional, translational and post-translational levels. The reprogramming of gene expression during EMT, as well as non-transcriptional changes, are initiated and controlled by signalling pathways that respond to extracellular cues. Among these, transforming growth factor-β (TGFβ) family signalling has a predominant role; however, the convergence of signalling pathways is essential for EMT.
doi:10.1038/nrm3758
PMCID: PMC4240281  PMID: 24556840

Results 1-25 (182)