Lipocalins are a structurally conserved and diversely functional family of proteins that are of potential importance in epididymis functions. The rat Lcn9 gene was cloned by in silico methods and genome walking based on homology to the rhesus monkey epididymal ESC513 and its polyclonal antisera were prepared. The rat Lcn9 gene is located on chromosome 3p13 spanning 7 exons, contains 2.3 kb and encodes 179 amino acids with a 17-amino acid signal peptide. Northern blot, western blot, and immunohistochemical staining analysis revealed that rat Lcn9 was a novel epididymis-specific gene, expressed selectively in the proximal caput region, influenced by luminal fluid testicular factors. Moreover, Lcn9 protein was modified by N-glycosylation and bound on the postacrosomal domain of caput sperm. In conclusion, the rat Lcn9 exhibited tissue-, region-, and temporal-specific expression patterns and its expression was regulated by luminal testicular factors. Its potential roles in sperm maturation are discussed.
epididymis; lipocalin; Lcn9 gene
Immunofluorescence assay (IFA) is one of the most frequently used methods in the biological sciences and clinic diagnosis, but it is expensive and time-consuming. To overcome these limitations, we developed a faster and more cost-effective IFA (f-IFA) by modifying the standard IFA, and applied this method to track the progression of human cytomegalovirus (HCMV) infection in different cells. The f-IFA that we developed not only saves time, but also dramatically reduces the quantity of antibody (Ab), which will facilitate the application of IFA in clinic diagnosis. f-IFA requires only 15 min for blocking, 10 min incubation for each primary and secondary Abs, followed by 1 min extensive wash after each incubation. Only 25 μl of diluted Ab solution was needed for each coverslip at the primary and secondary Ab incubation steps. In addition, all steps were performed at room temperature. This f-IFA has been applied successfully to follow virion entry (pp65) and expression of viral genes (IE1, UL44, and pp65) in order to track the details of HCMV infection process. We found that ∼0.5% HCMV-infected T98G cells formed multiple-micronuclei (IE1 and nucleus staining) and had virus shedding (pp65 staining) by f-IFA, which could not be detected by the traditional IFA. Our results indicated that f-IFA is a sensitive, convenient, fast, and cost-effective method for investigating the details of virus infection progress, especially HCMV infection. The faster and cost-effective feature with higher sensitivity and specificity implies that f-IFA has potential applications in clinical diagnosis.
immunofluorescence assay; human cytomegalovirus; virus entry; viral gene expression; virus replication
Janus kinase (JAK)-signal transducer and activators of transcription (STAT) signaling pathways play crucial roles in lymphopoiesis. In particular, JAK3 has unique functions in the lymphoid system such that JAK3 ablation results in phenotypes resembling severe combined immunodeficiency syndrome. This review focuses on the biochemistry, immunological functions, and clinical significance of JAK3. Compared with other members of the JAK family, the biochemical properties of JAK3 are relatively less well characterized and thus largely inferred from studies of JAK2. Furthermore, new findings concerning the cross-talks between Notch and JAK signaling pathways through ubiquitin-mediated protein degradation are discussed in more detail.
JAK3; Notch; Asb2; JAK2
The discovery of RNA interference (RNAi) has revolutionized genetic analysis in mammalian cells. Loss-of-function RNAi screens enable rapid, functional annotation of the genome. Of the various RNAi approaches, pooled shRNA libraries have received considerable attention because of their versatility. A number of genome-wide shRNA libraries have been constructed against the human and mouse genomes, and these libraries can be readily applied to a variety of screens to interrogate the function of human and mouse genes in an unbiased fashion. We provide an introduction to the technical aspects of using pooled shRNA libraries for genetic screens.
shRNA library; pooled screen; RNAi
During mammalian development, cardiac specification and ultimately lineage commitment to a specific cardiac cell type is accomplished by the action of specific transcription factors (TFs) and their meticulous control on an epigenetic level. In this review, we detail how cardiac-specific TFs function in concert with nucleosome remodeling and histone-modifying enzymes to regulate a diverse network of genes required for processes such as cell growth and proliferation, or epithelial to mesenchymal transition (EMT), for instance. We provide examples of how several cardiac TFs, such as Nkx2.5, WHSC1, Tbx5, and Tbx1, which are associated with developmental and congenital heart defects, are required for the recruitment of histone modifiers, such as Jarid2, p300, and Ash2l, and components of ATP-dependent remodeling enzymes like Brg1, Baf60c, and Baf180. Binding of these TFs to their respective sites at cardiac genes coincides with a distinct pattern of histone marks, indicating that the precise regulation of cardiac gene networks is orchestrated by interactions between TFs and epigenetic modifiers. Furthermore, we speculate that an epigenetic signature, comprised of TF occupancy, histone modifications, and overall chromatin organization, is an underlying mechanism that governs cardiac morphogenesis and disease.
epigenetics; histone modifications; DNA methylation; congenital heart disease
Chromatin is organized into distinct functional domains. During mitotic cell division, both genetic information encoded in DNA sequence and epigenetic information embedded in chromatin structure must be faithfully duplicated. The inheritance of epigenetic states is critical in maintaining the genome integrity and gene expression state. In this review, we will discuss recent progress on how proteins known to be involved in DNA replication and DNA replication-coupled nucleosome assembly impact on the inheritance and maintenance of heterochromatin, a tightly compact chromatin structure that silences gene transcription. As heterochromatin is important in regulating gene expression and maintaining genome stability, understanding how heterochromatin states are inherited during S phase of the cell cycle is of fundamental importance.
epigenetic inheritance; DNA replication; DNA replication-coupled nucleosome assembly; heterochromatin silencing
During the last decade, we saw an explosion of studies investigating the role of lysine methylation/demethylation of histones and non-histone proteins, such as p53, NF-kappaB, and E2F1. These ‘Ying-Yang’ post-translational modifications are important to fine-tuning the activity of these proteins. Lysine methylation and demethylation are catalyzed by protein lysine methyltransferases (PKMTs) and protein lysine demethylases (PKDMs). PKMTs, PKDMs, and their substrates have been shown to play important roles in cancers. Although the underlying mechanisms of tumorigenesis are still largely unknown, growing evidence is starting to link aberrant regulation of methylation to tumorigenesis. This review focuses on summarizing the recent progress in understanding of the function of protein lysine methylation, and in the discovery of small molecule inhibitors for PKMTs and PKDMs. We also discuss the potential and the caveats of targeting protein lysine methylation for the treatment of cancer.
methylation; demethylation; methyltransferase; demethylase; cancer; epigenetics
An increasing number of cyclopeptides have been discovered as products of ribosomal synthetic pathway. The biosynthetic study of these cyclopeptides has revealed interesting new mechanisms for cyclization. This review highlighted the recent discoveries in cyclization mechanisms for cyclopeptides synthesized independently of non-ribosomal peptide synthetases, including endopeptidase-catalyzed cyclization, intein-mediated cyclization, and peptide synthetase-catalyzed cyclization. This information may help to design hybrid ribosomal and non-ribosomal biosynthetic systems to produce novel cyclopeptides with various bioactivities.
ribosomal peptide; cyclopeptides; non-ribosomal peptide synthetase; cyclization mechanism
The mammalian target of rapamycin (mTOR) is an evolutionarily conserved serine/threonine protein kinase that regulates numerous cellular processes including cell growth, proliferation, cell cycle, and autophagy. mTOR forms two different multi-protein complexes referred to as mTOR complex 1 (mTORC1) and mTORC2, and each complex exerts distinct functions exclusively. mTORC1 activity is sensitive to the selective inhibitor rapamycin, whereas mTORC2 is resistant. mTORC1 is regulated by many intra- and extra-cellular cues such as growth factors, nutrients, and energy-sensing signals, while mTORC2 senses ribosome maturation and growth factor signaling. This review focuses on current understandings by which mTORC1 pathway senses cellular nutrient availability for its activation.
mTORC1; amino acids; rapamycin; Rag GTPase
Histone ubiquitination regulates the chromatin structure that is important for many biological processes. Recently, ubiquitination of histones was observed during the DNA damage response (DDR), and this modification is controlled by really interesting new gene (RING) domain E3 ligase, RNF8. Together with the E2 conjugating enzyme UBC13, RNF8 catalyzes ubiquitination of the histones H2A and H2AX during the DDR, thus facilitating downstream recruitment of DDR factors, such as p53 binding protein 1 (53BP1) and breast cancer type 1 susceptibility protein (BRCA1), to the damage site. Accordingly, the RNF8 knockout mice display phenotypes associated with failed DDR, including hypersensitivity to ionizing radiation, V(D)J recombination deficiency, and a predisposition to cancer. In addition to the DDR phenotypes, RNF8 knockout mice fail to generate mature sperm during spermatogenesis, resulting in male sterility. The RNF8 knockout mice also have a drastic reduction in histone ubiquitination in the testes. These findings indicate that the role of histone ubiquitination during chromatin remodeling in two different biological events could be linked by an RNF8-dependent mechanism. Here, we review the molecular mechanism of RNF8-dependent histone ubiquitination both in DDR and spermatogenesis.
acetylation; RNF8; UBC13; chromatin remodeling
Chronic disruption of energy balance, where energy intake exceeds expenditure, is a major risk factor for the development of metabolic syndrome. The latter is characterized by a constellation of symptoms including obesity, dyslipidemia, insulin resistance, hypertension, and non-alcoholic fatty liver disease. Altered expression of genes involved in glucose and lipid metabolism as well as mitochondrial oxidative phosphorylation has been implicated in the pathogenesis of these disorders. The peroxisome proliferator-activated receptor γ coactivator-1 (PGC-1) family of transcriptional coactivators is emerging as a hub linking nutritional and hormonal signals and energy metabolism. PGC-1α and PGC-1β are highly responsive to environmental cues and coordinate metabolic gene programs through interaction with transcription factors and chromatin-remodeling proteins. PGC-1α has been implicated in the pathogenic conditions including obesity, type 2 diabetes, neurodegeneration, and cardiomyopathy, whereas PGC-1β plays an important role in plasma lipoprotein homeostasis and serves as a hepatic target for niacin, a potent hypotriglyceridemic drug. Here, we review recent advances in the identification of physiological and pathophysiological contexts involving PGC-1 coactivators, and also discuss their implications for therapeutic development.
transcriptional coactivator; metabolic syndrome; PGC-1; mitochondrial biogenesis; energy metabolism
α-Conotoxins are small disulfide-constrained peptides that act as potent and selective antagonists on specific subtypes of nicotinic acetylcholine receptors (nAChRs). We previously cloned two α-conotoxins, Mr1.1 from the molluscivorous Conus marmoreus and Lp1.4 from the vermivorous Conus leopardus. Both of them have the typical 4/7-type framework of the subfamily of α-conotoxins that act on neuronal nAChRs. In this work, we chemically synthesized these two toxins and characterized their functional properties. The synthetic Mr1.1 could primarily inhibit acetylcholine (ACh)-evoked currents reversibly in the oocyte-expressed rat α7 nAChR, whereas Lp1.4 was an unexpected specific blocker of the mouse fetal muscle α1β1γδ receptor. Although their inhibition affinities were relatively low, their unique receptor recognition profiles make them valuable tools for toxin-receptor interaction studies. Mr1.1 could also suppress the inflammatory response to pain in vivo, suggesting that it should be further investigated with respect to its molecular role in analgesia and its mechanism or therapeutic target for the treatment of pain.
Conus; α4/7-conotoxin; nicotinic acetylcholine receptor; analgesic
Colon cancer is a common malignant tumor that is associated with increased morbidity and mortality. Nasopharyngeal carcinoma-associated gene 6 (NGX6) is a novel candidate suppressor gene of tumor metastasis, which is down-regulated in colon cancer. This study was designed to investigate the roles of NGX6 on the growth and invasiveness of human colon cancer cell line, HT-29, and to elucidate the molecular mechanism of their action. Results showed that NGX6 could inhibit the invasiveness and extracellular matrix adhesion of HT-29 cells and restore the gap junctional intercellular communication of cells. Moreover, NGX6 could suppress the translocation of β-catenin from nucleus and cytoplasm to plasma membrane, inhibit the activity of TCF4 transcript factor, and down-regulate the expression of Wnt-direct-targeted genes c-myc, cyclin D1 and COX-2. We suggested that NGX6 inhibits cell invasion and adhesion through the suppression of Wnt signal pathway in colon cancer.
NGX6; colon carcinoma; Wnt/β-catenin signaling pathway; metastasis
Hypothalamic histaminergic tuberomammillary (TM) neurons express nicotinic acetylcholine receptors (nAChRs) with kinetic and pharmacological properties resembling those of highly Ca2+ permeable α7 nAChRs. However, the Ca2+ permeability of TM nAChR channels has not been determined. To directly evaluate the Ca2+ permeability of TM nAChRs, patch-clamp recordings were conducted using non-cultured acutely dissociated TM neurons and external solutions containing low (2 mM) and high (20 mM) concentrations of Ca2+. A shift in the reversal potentials was determined from the current–voltage relationships and the permeability ratio, PCa/PNa, was estimated within the Goldman-Hodgkin-Katz constant field approximation. TM nAChRs were found to be highly Ca2+ permeable with the permeability ratio, PCa/PNa(nAChR) being ∼5.9 and the fractional Ca2+ current, Pf(nAChR) being ∼10.1% at −60 mV. As a positive control for the applied methods and analysis, the permeability ratio, PCa/PNa(NMDAR) being ∼8.3 and the fractional Ca2+ current, Pf(NMDAR) being ∼13.6% at −60 mV for NMDA receptors were determined using non-cultured acutely dissociated hippocampal pyramidal neurons and found similar to previously reported values. Therefore, these results demonstrate that native TM nAChRs are highly Ca2+ permeable, but ∼1.4 fold less permeable to Ca2+ than native hippocampal pyramidal NMDA receptors.
alpha7; nAChR; hypothalamic; permeability; calcium
Chemerin is a novel chemoattractant recognized by chemokine-like receptor 1 (CMKLR1), a serpentine receptor expressed primarily by plasmacytoid dendritic cells, natural killer cells, and macrophages. Human prochemerin circulates in plasma as an inactive precursor. Its chemotactic activity is expressed upon cleavage of the C-terminal amino acid residues by proteases of the coagulation, fibrinolytic, and inflammatory system. The C-terminal cleavage site of prochemerin is highly conservative, indicating that the proteolytic regulation of chemerin bioactivity is a common mechanism undertaken by different species. In this review, we summarized chemerin–proteases interactions, chemerin receptors, and their importance in normal and pathologic conditions.
chemerin; proteolysis; chemotactic; inflammation
Epithelial-mesenchymal transition (EMT) is a key step during embryonic morphogenesis, heart development, chronic degenerative fibrosis, and cancer metastasis. Several distinct traits have been conveyed by EMT, including cell motility, invasiveness, resistance to apoptosis, and some properties of stem cells. Many signal pathways have contributed to the induction of EMT, such as transforming growth factor-β, Wnt, Hedgehog, Notch, and nuclear factor κB. Over the last few years, increasing evidence has shown that EMT plays an essential role in tumor progression and metastasis. Understanding the molecular mechanism of EMT has a great effect in unraveling the metastatic cascade and may lead to novel interventions for metastatic disease.
epithelial-mesenchymal transition; metastasis; Snail; Twist; signal transduction
Krüppel-like factor 4 is a zinc finger-type transcription factor expressed in a variety of tissues, including the epithelium of intestine and the skin, where it is important in differentiation and cell cycle arrest. KLF4 can both activate and repress transcription, depending on the gene targeted. Moreover, KLF4 can function as a tumor suppressor or an oncogene, depending on the cellular context. Finally, KLF4 is important in reprogramming differentiated fibroblasts into inducible pluripotent stem cells, which highly resemble embryonic stem cells. This review will summarize what is known about the diverse functions of KLF4, as well as their molecular mechanisms.
Krüppel-like factor 4; colorectal cancer; stem cell
cAMP-mediated signaling pathways regulate a multitude of important biological processes under both physiological and pathological conditions, including diabetes, heart failure, and cancer. In eukaryotic cells, the effects of cAMP are mediated by two ubiquitously expressed intracellular cAMP receptors, the classic protein kinase A/cAMP-dependent protein kinase (PKA/cAPK) and the recently discovered exchange protein directly activated by cAMP/cAMP-regulated guanine nucleotide exchange factors (Epac/cAMP-GEF). Like PKA, Epac contains an evolutionally conserved cAMP-binding domain that acts as a molecular switch for sensing intracellular second messenger cAMP levels to control diverse biological functions. The existence of two families of cAMP effectors provides a mechanism for a more precise and integrated control of the cAMP signaling pathways in a spatial and temporal manner. Depending upon their relative abundance, distribution and localization, as well as the specific cellular environments, Epac and PKA may act independently, converge synergistically, or oppose each other in regulating a specific cellular function.
cyclic AMP; exchange protein directly activated by cAMP (Epac)/cAMP-regulated guanine exchange factor (cAMP-GEF); protein kinase A (PKA)/cAMP-dependent protein kinase (cAPK); signal transduction
Since the introduction of the concepts of allostery about four decades ago, much advancement has been made in elucidating the structure-function correlation in allostery. However, there are still a number of issues that remain unresolved. In this review we employed mammalian pyruvate kinase (PK) as a model system to understand the role of protein dynamics in modulating cooperativity. PK has a TIM (α/β)8 barrel structural motif. PK is an ideal system to address basic questions regarding regulatory mechanisms about this common (α/β)8 structural motif. The simplest model accounting for all the solution thermodynamic and kinetic data on ligand-enzyme interactions involves two conformational states, inactive ET and active ER. These conformational states are represented by domain movements. Further studies provide the first evidence for a differential effect of ligand binding on the dynamics of the structural elements, not major secondary structural changes. These data are consistent with our model that allosteric regulation of PK is the consequence of perturbation of the distribution of an ensemble of states in which the inactive ET and active ER represent the two extreme end states. Sequence differences and ligands can modulate the distribution of states leading to alterations of functions. The future work includes: defining the network of functionally connected residues; elucidate the chemical principles governing the sequence differences which affect functions; and probe the nature of mutations on the stability of the secondary structural elements which in turn modulate allostery.
allostery; thermodynamics; protein dynamics; protein fold; human genetics
Since the first Wnt gene was identified in 1982, the functions and mechanisms of Wnt signaling have been extensively studied. Wnt signaling is conserved from invertebrates to vertebrates and regulates early embryonic development as well as the homeostasis of adult tissues. In addition, both embryonic stem cells and adult stem cells are regulated by Wnt signaling. Deregulation of Wnt signaling is associated with many human diseases, particularly cancer. In this review, we will discuss in detail the functions of many components involved in the Wnt signal transduction pathway. Then, we will explore what is known about the role of Wnt signaling in stem cells and cancer.
Wnt; β-catenin; cancer; stem cell
The hedgehog pathway, initially discovered by two laureates Drs. E. Wieschaus and C. Nusslein-Volhard in Drosophila, is a major regulator for cell differentiation, tissue polarity and cell proliferation. Studies from many laboratories including ours reveal activation of this pathway in most basal cell carcinomas and approximately 30% of extracutaneous human cancers, including medulloblastomas, gastrointestinal, lung, breast and prostate cancers. Thus, it is believed that targeted inhibition of hedgehog signaling may be effective in treatment and prevention in many types of human cancers. Even more exciting is the discovery and synthesis of specific signaling antagonists for the hedgehog pathway, which have significant clinical implications in novel cancer therapeutics. In this review, we will review major advanced in our understanding of hedgehog signaling activation in different types of human cancers, molecular basis of hedgehog signaling activation, major antagonists for hedgehog signaling inhibition and their potential conical application in human cancer therapy.
hedgehog; smoothened; PTCH1; human cancer therapy; basal cell carcinomas; antagonist
The accurate formation of cognate aminoacyl-tRNAs (aa-tRNAs) is essential for the fidelity of translation. Most amino acids are esterified onto their cognate tRNA isoacceptors directly by aminoacyl-tRNA synthetases (aaRSs). However, in the case of four amino acids (Gln, Asn, Cys and Sec), aminoacyl-tRNAs are made through indirect pathways in many organisms across all three domains of life. The process begins with the charging of noncognate amino acids to tRNAs by a specialized synthetase in the case of Cys-tRNACys formation or by synthetases with relaxed specificity such as the non-discriminating glutamyl-tRNA synthetase (ND-GluRS), non-discriminating aspartyl-tRNA synthetase (ND-AspRS) and seryl-tRNA synthetase (SerRS). The resulting misacylated tRNAs are then converted to cognate pairs through transformation of the amino acids on the tRNA, which is catalyzed by a group of tRNA-dependent modifying enzymes such as tRNA-dependent amidotransferases, Sep-tRNA:Cys-tRNA synthase (SepCysS), O-phosphoseryl-tRNA kinase (PSTK) and Sep-tRNA:Sec-tRNA synthase (SepSecS). The majority of these indirect pathways are widely spread in all domains of life and thought to be ancient in the course of evolution.
aminoacyl-tRNA; indirect pathways; tRNA-dependent amidotransferase; tRNA-dependent cysteine biosynthesis; selenocysteine biosynthesis