氨基酰tRNA合成酶的经典与非经典酶活性

氨基酰tRNA合成酶（aminoacyl-tRNA synthetases,aaRS）家族的经典功能是催化氨基酸与对应tRNA结合,形成氨基酰tRNA,参与蛋白质合成。aaRS在进化过程中不断增加与氨基酰化功能无关的新结构域,其亚细胞器定位也受到营养、压力信号、参与调控血管新生和炎症反应等内外部信号调控,且不同aaRS的突变导致不同人类疾病,提示aaRS具有信号传导功能,但缺少具体的生化机制。最新发现aaRS具有氨基酰转移酶活性。一种氨基酸可以被其对应的aaRS活化成氨基酰AMP,氨基酰AMP可以修饰与该aaRS相互作用蛋白质的赖氨酸,传递该氨基酸的丰度及结构信息,调控细胞信号网络。aaRS新功能的发现和研究,为解释aaRS的生理病理重要性提供新的方向。本文综述aaRS的进化及非经典功能,讨论aaRS氨基酰转移酶活性在细胞信号传导及其与疾病的相关性,也包括药物开发潜力。     

Making sense out of missense mutations: Mechanistic dissection of Notch receptors through structure-function studies in Drosophila

Notch signaling is involved in the development of almost all organ systems and is required post-developmentally to modulate tissue homeostasis. Rare variants in Notch signaling pathway genes are found in patients with rare Mendelian disorders, while unique or recurrent somatic mutations in a similar set of genes are identified in cancer. The human genome contains four genes that encode Notch receptors, NOTCH1-4, all of which are linked to genetic diseases and cancer. Although some mutations have been classified as clear loss- or gain-of-function alleles based on cellular or rodent based assay systems, the functional consequence of many variants/mutations in human Notch receptors remain unknown. In this review, I will first provide an overview of the domain structure of Notch receptors and discuss how each module is known to regulate Notch signaling activity in vivo using the Drosophila Notch receptor as an example. Next, I will introduce some interesting mutant alleles that have been isolated in the fly Notch gene over the past > 100 years of research and discuss how studies of these mutations have facilitated the understanding of Notch biology. By identifying unique alleles of the fly Notch gene through forward genetic screens, mapping their molecular lesions and characterizing their phenotypes in depth, one can begin to unravel new mechanistic insights into how different domains of Notch fine-tune signaling output. Such information can be useful in deciphering the functional consequences of rare variants/mutations in human Notch receptors, which in turn can influence disease management and therapy.     

Glial response to polyglutamine-mediated stress

Neurodegenerative trinucleotide (CAG) repeat disorders are caused by the expansion of polyglutamine tracts within the disease proteins. Some of these proteins have an unknown function. How expanded polyglutamine causes target neurons to degenerate is not clear. Recent evidence suggests that intercellular miscommunication may contribute to polyglutamine pathogenesis in CAG repeat disorders. Polyglutamine induced degeneration of the target neuron can be mediated via glia-neuron interactions. Here we hypothesize that during the neurodegenerative process the failure of cell-cell interactions have more severe consequences than alterations in intracellular neuron biology. We further believe that bidirectional communication between neurons and glia is a prerequisite for the normal development and function of either cell type. Understanding intercellular signaling mechanisms such as glial trophic factors and their receptors, cell adhesion or other well-defined signaling molecules provides opportunities for developing potential therapies.     

Assessing systems properties of yeast mitochondria through an interaction map of the organelle

Mitochondria carry out specialized functions; compartmentalized, yet integrated into the metabolic and signaling processes of the cell. Although many mitochondrial proteins have been identified, understanding their functional interrelationships has been a challenge. Here we construct a comprehensive network of the mitochondrial system. We integrated genome-wide datasets to generate an accurate and inclusive mitochondrial parts list. Together with benchmarked measures of protein interactions, a network of mitochondria was constructed in their cellular context, including extra-mitochondrial proteins. This network also integrates data from different organisms to expand the known mitochondrial biology beyond the information in the existing databases. Our network brings together annotated and predicted functions into a single framework. This enabled, for the entire system, a survey of mutant phenotypes, gene regulation, evolution, and disease susceptibility. Furthermore, we experimentally validated the localization of several candidate proteins and derived novel functional contexts for hundreds of uncharacterized proteins. Our network thus advances the understanding of the mitochondrial system in yeast and identifies properties of genes underlying human mitochondrial disorders.     

Human diseases: clues to cracking the connexin code?

The vertebrate gap junctions formed by the connexin family of transmembrane proteins came to the attention of geneticists in 1993 with the identification of mutations linked to a form of demyelinating neuropathy. Since then, several other genetic disorders have been linked to mutations in specific connexin genes. Also, different diseases can result from different mutations in the same connexin gene. In addition, specific connexin knockout mice have surprising phenotypes. This is leading cell biologists to look afresh at connexins and their involvement in intercellular communication through gap junctions, a process that seems central to coordinating cell function within tissues. Here, we comment on how genetic studies are giving a new impetus to the cell biology of gap junctions.     

The nuclear lamina and inherited disease

Inherited disorders of the nuclear lamina present some of the most intriguing puzzles in cell biology. Mutations in lamin A and lamin C – nuclear intermediate filament proteins that are expressed in nearly all somatic cells – cause tissue-specific diseases that affect striated muscle, adipose tissue and peripheral nerve or skeletal development. Recent studies provide clues about how different mutations in these proteins cause either muscle disease or partial lipodystrophy. Although the precise pathogenic mechanisms are currently unknown, the involvement of lamins in several different disorders shows that research on the nuclear lamina will shed light on common human pathologies.     

Emerging evidence implicating a role for neurexins in neurodegenerative and neuropsychiatric disorders

Synaptopathies are brain disorders characterized by dysfunctional synapses, which are specialized junctions between neurons that are essential for the transmission of information. Synaptic dysfunction can occur due to mutations that alter the structure and function of synaptic components or abnormal expression levels of a synaptic protein. One class of synaptic proteins that are essential to their biology are cell adhesion proteins that connect the pre- and post-synaptic compartments. Neurexins are one type of synaptic cell adhesion molecule that have, recently, gained more pathological interest. Variants in both neurexins and their common binding partners, neuroligins, have been associated with several neuropsychiatric disorders. In this review, we summarize some of the key physiological functions of the neurexin protein family and the protein networks they are involved in. Furthermore, examination of published literature has implicated neurexins in both neuropsychiatric and neurodegenerative disorders. There is a clear link between neurexins and neuropsychiatric disorders, such as autism spectrum disorder and schizophrenia. However, multiple expression studies have also shown changes in neurexin expression in several neurodegenerative disorders, including Alzheimer''s disease and Parkinson''s disease. Therefore, this review highlights the potential importance of neurexins in brain disorders and the importance of doing more targeted studies on these genes and proteins.     

Notch and presenilins in vertebrates and invertebrates: implications for neuronal development and degeneration

Recent progress in elucidating the biology of Notch and presenilin has revealed a close functional relationship between these two proteins during cell fate determination in worms, flies and humans. Presenilins are required for the putatively intramembranous proteolysis of Notch to release its intracellular domain to the nucleus. This finding establishes a specific biochemical role for presenilins in Notch signaling and interfaces with emerging evidence about how frizzled, disheveled and numerous other genes regulate the highly complex Notch pathway. Advances in understanding Notch and presenilin functions in the differentiation of neurons and non-neural cells have important implications not only for development but also for late-life degenerative disorders such as Alzheimer's disease.     

Functional discovery via a compendium of expression profiles

Ascertaining the impact of uncharacterized perturbations on the cell is a fundamental problem in biology. Here, we describe how a single assay can be used to monitor hundreds of different cellular functions simultaneously. We constructed a reference database or "compendium" of expression profiles corresponding to 300 diverse mutations and chemical treatments in S. cerevisiae, and we show that the cellular pathways affected can be determined by pattern matching, even among very subtle profiles. The utility of this approach is validated by examining profiles caused by deletions of uncharacterized genes: we identify and experimentally confirm that eight uncharacterized open reading frames encode proteins required for sterol metabolism, cell wall function, mitochondrial respiration, or protein synthesis. We also show that the compendium can be used to characterize pharmacological perturbations by identifying a novel target of the commonly used drug dyclonine.     

FIP200, a key signaling node to coordinately regulate various cellular processes

A central question in cell biology is how various cellular processes are coordinately regulated in normal cell and how dysregulation of the normal signaling pathways leads to diseases such as cancer. Recent studies have identified FIP200 as a crucial signaling component to coordinately regulate different cellular events by its interaction with multiple signaling pathways. This review will focus on the cellular functions of FIP200 and its interacting proteins, as well as the emerging roles of FIP200 in embryogenesis and cancer development. Further understanding of FIP200 function might provide novel therapeutic targets for human diseases such as cancer.     

A molecular clamp ensures allosteric coordination of peptidyltransfer and ligand binding to the ribosomal A-site

Although the ribosome is mainly comprised of rRNA and many of its critical functions occur through RNA–RNA interactions, distinct domains of ribosomal proteins also participate in switching the ribosome between different conformational/functional states. Prior studies demonstrated that two extended domains of ribosomal protein L3 form an allosteric switch between the pre- and post-translocational states. Missing was an explanation for how the movements of these domains are communicated among the ribosome''s functional centers. Here, a third domain of L3 called the basic thumb, that protrudes roughly perpendicular from the W-finger and is nestled in the center of a cagelike structure formed by elements from three separate domains of the large subunit rRNA is investigated. Mutagenesis of basically charged amino acids of the basic thumb to alanines followed by detailed analyses suggests that it acts as a molecular clamp, playing a role in allosterically communicating the ribosome''s tRNA occupancy status to the elongation factor binding region and the peptidyltransferase center, facilitating coordination of their functions through the elongation cycle. The observation that these mutations affected translational fidelity, virus propagation and cell growth demonstrates how small structural changes at the atomic scale can propagate outward to broadly impact the biology of cell.     

The LKB1 tumor suppressor kinase in human disease

Inactivating germline mutations in the LKB1 gene underlie Peutz-Jeghers syndrome characterized by hamartomatous polyps and an elevated risk for cancer. Recent studies suggest the involvement of LKB1 also in more common human disorders including diabetes and in a significant fraction of lung adenocarcinomas. These observations have increased the interest towards signaling pathways of this tumor suppressor kinase. The recent breakthroughs in understanding the molecular functions of the LKB1 indicate its contribution as a regulator of cell polarity, energy metabolism and cell proliferation. Here we review how the substrates and cellular functions of LKB1 may be linked to Peutz-Jeghers syndrome and other diseases, and discuss how some of the molecular changes associated with altered LKB1 signaling might be used in therapeutic approaches.     

Tuberous sclerosis complex: from Drosophila to human disease

Tuberous sclerosis complex (TSC) is a human syndrome characterized by a widespread development of benign tumors. This disease is caused by mutations in the TSC1 or TSC2 tumor suppressor genes; the molecular mechanisms underlying the activity of these have long been elusive. Recent studies of Drosophila and mammalian cells demonstrate that the TSC1-TSC2 complex functions as GTPase activating protein against Rheb - a Ras-like small GTPase, which in turn regulates TOR signaling in nutrient-stimulated cell growth. These findings provide a new paradigm for how proteins involved in nutrient sensing could function as tumor suppressors and suggest novel therapeutic targets against TSC. Here, we review these exciting developments with an emphasis on Drosophila studies and discuss how Drosophila can be a powerful model system for an understanding of the molecular mechanisms of the activity of human disease genes.     

Synapse development in health and disease

Recent insights into the genetic basis of neurological disease have led to the hypothesis that molecular pathways involved in synaptic growth, development, and stability are perturbed in a variety of mental disorders. Formation of a functional synapse is a complex process requiring stabilization of initial synaptic contacts by adhesive protein interactions, organization of presynaptic and postsynaptic specializations by scaffolding proteins, regulation of growth by intercellular signaling pathways, reorganization of the actin cytoskeleton, and proper endosomal trafficking of synaptic growth signaling complexes. Many neuropsychiatric disorders, including autism, schizophrenia, and intellectual disability, have been linked to inherited mutations which perturb these processes. Our understanding of the basic biology of synaptogenesis is therefore critical to unraveling the pathogenesis of neuropsychiatric disorders.     

The Cell Biology of the Endocytic System from an Evolutionary Perspective

Evolutionary cell biology can afford an interdisciplinary comparative view that gives insights into both the functioning of modern cells and the origins of cellular systems, including the endocytic organelles. Here, we explore several recent evolutionary cell biology studies, highlighting investigations into the origin and diversity of endocytic systems in eukaryotes. Beginning with a brief overview of the eukaryote tree of life, we show how understanding the endocytic machinery in a select, but diverse, array of organisms provides insights into endocytic system origins and predicts the likely configuration in the last eukaryotic common ancestor (LECA). Next, we consider three examples in which a comparative approach yielded insight into the function of modern cellular systems. First, using ESCRT-0 as an example, we show how comparative cell biology can discover both lineage-specific novelties (ESCRT-0) as well as previously ignored ancient proteins (Tom1), likely of both evolutionary and functional importance. Second, we highlight the power of comparative cell biology for discovery of previously ignored but potentially ancient complexes (AP5). Finally, using examples from ciliates and trypanosomes, we show that not all organisms possess canonical endocytic pathways, but instead likely evolved lineage-specific mechanisms. Drawing from these case studies, we conclude that a comparative approach is a powerful strategy for advancing knowledge about the general mechanisms and functions of endocytic systems.The endomembrane system mediates transport of lipids, proteins, and other molecules to the various locations in the eukaryotic cell. It also underlies the interactions with the extracellular environment, presenting material at the cell surface as well as secreting and internalizing material. In modern cells, these latter aspects are important for signal transduction, surface remodeling, and nutrient acquisition. Just as these abilities are crucial to modern cells, they were likely equally important for the very first eukaryotes as they underwent speciation from prokaryotic-like ancestors via niche competition in the ancient world (Cavalier-Smith 2002). Understanding the events and biological processes involved in the evolution of the membrane-trafficking system in general, and the endocytic system in particular, gives us insights into landmark events in our cellular past.Evolutionary insight about cellular phenomenon is derived from two basic types of comparative study: from molecular cell biological analyses of increasingly tractable model organisms across the diversity of eukaryotes, and by computational analyses of genomic information (i.e., the genes encoding the membrane-trafficking machinery). Whereas the information gathered from taking this comparative, or evolutionary cell biology, approach (Brodsky et al. 2012) is valuable for evolutionary content, these same analyses are potentially highly valuable in understanding basic cell biology, a benefit that is perhaps less obvious and hence less appreciated. In this article, we frame what has been learned about the evolution of the endocytic system, in the dual context of what it tells us about ancient cells together with what it can tell us about modern ones. We begin with a brief introduction to eukaryotic diversity and the evolution of the membrane-trafficking system. We then delve into the evolution of specific endocytic factors to illustrate the ways in which cell biologists of all stripes can benefit from the emerging field of evolutionary cell biology.     

Plant-mPLoc: A Top-Down Strategy to Augment the Power for Predicting Plant Protein Subcellular Localization

One of the fundamental goals in proteomics and cell biology is to identify the functions of proteins in various cellular organelles and pathways. Information of subcellular locations of proteins can provide useful insights for revealing their functions and understanding how they interact with each other in cellular network systems. Most of the existing methods in predicting plant protein subcellular localization can only cover three or four location sites, and none of them can be used to deal with multiplex plant proteins that can simultaneously exist at two, or move between, two or more different location sites. Actually, such multiplex proteins might have special biological functions worthy of particular notice. The present study was devoted to improve the existing plant protein subcellular location predictors from the aforementioned two aspects. A new predictor called “Plant-mPLoc” is developed by integrating the gene ontology information, functional domain information, and sequential evolutionary information through three different modes of pseudo amino acid composition. It can be used to identify plant proteins among the following 12 location sites: (1) cell membrane, (2) cell wall, (3) chloroplast, (4) cytoplasm, (5) endoplasmic reticulum, (6) extracellular, (7) Golgi apparatus, (8) mitochondrion, (9) nucleus, (10) peroxisome, (11) plastid, and (12) vacuole. Compared with the existing methods for predicting plant protein subcellular localization, the new predictor is much more powerful and flexible. Particularly, it also has the capacity to deal with multiple-location proteins, which is beyond the reach of any existing predictors specialized for identifying plant protein subcellular localization. As a user-friendly web-server, Plant-mPLoc is freely accessible at http://www.csbio.sjtu.edu.cn/bioinf/plant-multi/. Moreover, for the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the web-server to get the desired results. It is anticipated that the Plant-mPLoc predictor as presented in this paper will become a very useful tool in plant science as well as all the relevant areas.     

Reduced affinity to and inhibition by DKK1 form a common mechanism by which high bone mass-associated missense mutations in LRP5 affect canonical Wnt signaling

The low-density-lipoprotein receptor-related protein 5 (LRP5), a coreceptor in the canonical Wnt signaling pathway, has been implicated in human disorders of low and high bone mass. Loss-of-function mutations cause the autosomal recessive osteoporosis-pseudoglioma syndrome, and heterozygous missense mutations in families segregating autosomal dominant high bone mass (HBM) phenotypes have been identified. We expressed seven different HBM-LRP5 missense mutations to delineate the mechanism by which they alter Wnt signaling. None of the mutations caused activation of the receptor in the absence of ligand. Each mutant receptor was able to reach the cell surface, albeit at differing amounts, and transduce exogenously supplied Wnt1 and Wnt3a signal. All HBM mutant proteins had reduced physical interaction with and reduced inhibition by DKK1. These data suggest that HBM mutant proteins can transit to the cell surface in sufficient quantity to transduce Wnt signal and that the likely mechanism for the HBM mutations' physiologic effects is via reduced affinity to and inhibition by DKK1.     

Emergent functions of proteins in non-stoichiometric supramolecular assemblies

Proteins are the basic functional units of the cell, carrying out myriads of functions essential for life. There are countless reports in molecular cell biology addressing the functioning of proteins under physiological and pathological conditions, aiming to understand life at the atomistic-molecular level and thereby being able to develop remedies against diseases. The central theme in most of these studies is that the functional unit under study is the protein itself. Recent rapid progress has radically challenged and extended this protein-function paradigm, by demonstrating that novel function(s) may emerge when proteins form dynamic and non-stoichiometric supramolecular assemblies. There is an increasing number of cases for such collective functions, such as targeting, localization, protection/shielding and filtering effects, as exemplified by signaling complexes and prions, biominerals and mucus, amphibian adhesions and bacterial biofilms, and a broad range of membraneless organelles (bio-condensates) formed by liquid-liquid phase separation in the cell. In this short review, we show that such non-stoichiometric organization may derive from the heterogeneity of the system, a mismatch in valency and/or geometry of the partners, and/or intrinsic structural disorder and multivalency of the component proteins. Either way, the resulting functional features cannot be simply described by, or predicted from, the properties of the isolated single protein(s), as they belong to the collection of proteins.