Since the sequencing of metazoan genomes began, it has become clear that the number of expressed proteins far exceeds the number of genes. It is now estimated that more than 98% of human genes give ...rise to multiple proteins through alternative pre-mRNA splicing. In this review, we highlight the known alternative splice variants of many channels, receptors, and growth factors that are important in nociception and pain. Recently, pharmacological control of alternative splicing has been proposed as potential therapy in cancer, wet age-related macular degeneration, retroviral infections, and pain. Thus, we also consider the effects that known splice variants of molecules key to nociception/pain have on nociceptive processing and/or analgesic action, and the potential for control of alternative pre-mRNA splicing as a novel analgesic strategy.
We review the evolution and structure of members of the transforming growth factor beta (TGF-beta) family, antagonistic or agonistic modulators, and receptors that regulate TGF-beta signaling in ...extracellular environments. The growth factor (GF) domain common to all family members and many of their antagonists evolved from a common cystine knot growth factor (CKGF) domain. The CKGF superfamily comprises six distinct families in primitive metazoans, including the TGF-beta and Dan families. Compared with Wnt/Frizzled and Notch/Delta families that also specify body axes, cell fate, tissues, and other families that contain CKGF domains that evolved in parallel, the TGF-beta family was the most fruitful in evolution. Complexes between the prodomains and GFs of the TGF-beta family suggest a new paradigm for regulating GF release by conversion from closed- to open-arm procomplex conformations. Ternary complexes of the final step in extracellular signaling show how TGF-beta GF dimers bind type I and type II receptors on the cell surface, and enable understanding of much of the specificity and promiscuity in extracellular signaling. However, structures suggest that when GFs bind repulsive guidance molecule (RGM) family coreceptors, type I receptors do not bind until reaching an intracellular, membrane-enveloped compartment, blurring the line between extra- and intracellular signaling. Modulator protein structures show how structurally diverse antagonists including follistatins, noggin, and members of the chordin family bind GFs to regulate signaling; complexes with the Dan family remain elusive. Much work is needed to understand how these molecular components assemble to form signaling hubs in extracellular environments in vivo.
Cys sub(2)His sub(2) zinc fingers (C2H2-ZFs) comprise the largest class of metazoan DNA-binding domains. Despite this domain's well-defined DNA-recognition interface, and its successful use in the ...design of chimeric proteins capable of targeting genomic regions of interest, much remains unknown about its DNA-binding landscape. To help bridge this gap in fundamental knowledge and to provide a resource for design-oriented applications, we screened large synthetic protein libraries to select binding C2H2-ZF domains for each possible three base pair target. The resulting data consist of >160 000 unique domain-DNA interactions and comprise the most comprehensive investigation of C2H2-ZF DNA-binding interactions to date. An integrated analysis of these independent screens yielded DNA-binding profiles for tens of thousands of domains and led to the successful design and prediction of C2H2-ZF DNA-binding specificities. Computational analyses uncovered important aspects of C2H2-ZF domain-DNA interactions, including the roles of within-finger context and domain position on base recognition. We observed the existence of numerous distinct binding strategies for each possible three base pair target and an apparent balance between affinity and specificity of binding. In sum, our comprehensive data help elucidate the complex binding landscape of C2H2-ZF domains and provide a foundation for efforts to determine, predict and engineer their DNA-binding specificities.
Cys sub(2)-His sub(2) zinc finger proteins (ZFPs) are the largest family of transcription factors in higher metazoans. They also represent the most diverse family with regards to the composition of ...their recognition sequences. Although there are a number of ZFPs with characterized DNA-binding preferences, the specificity of the vast majority of ZFPs is unknown and cannot be directly inferred by homology due to the diversity of recognition residues present within individual fingers. Given the large number of unique zinc fingers and assemblies present across eukaryotes, a comprehensive predictive recognition model that could accurately estimate the DNA-binding specificity of any ZFP based on its amino acid sequence would have great utility. Toward this goal, we have used the DNA-binding specificities of 678 two-finger modules from both natural and artificial sources to construct a random forest-based predictive model for ZFP recognition. We find that our recognition model outperforms previously described determinant-based recognition models for ZFPs, and can successfully estimate the specificity of naturally occurring ZFPs with previously defined specificities.
All sulfation reactions rely on active sulfate in the form of 3'-phospho-adenosine-5'-phospho sulfate (PAPS). In fungi, bacteria, and plants, the enzymes responsible for PAPS synthesis, ATP ...sulfurylase and adenosine-5'-phosphosulfate (APS) kinase, reside on separate polypeptide chains. In metazoans, however, bifunctional PAPS synthases catalyze the consecutive steps of sulfate activation by converting sulfate to PAPS via the intermediate APS. This intricate molecule and the related nucleotides PAPS and 3'-phospho-adenosine-5'-phospha te modulate the function of various enzymes from sulfation pathways, and these effects are summarized in this review. On the ATP sulfurylase domain that initially produces APS from sulfate and ATP, APS acts as a potent product inhibitor, being competitive with both ATP and sulfate. For the APS kinase domain that phosphorylates APS to PAPS, APS is an uncompetitive substrate inhibitor that can bind both at the ATP/ADP-binding site and the PAPS/APS-binding site. For human PAPS synthase 1, the steady-state concentration of APS has been modelled to be 1.6 mu m, but this may increase up to 60 mu m under conditions of sulfate excess. It is noteworthy that the APS concentration for maximal APS kinase activity is 15 mu m. Finally, we recognized APS as a highly specific stabilizer of bifunctional PAPS synthases. APS most likely stabilizes the APS kinase part of these proteins by forming a dead-end enzyme-ADP-APS complex at APS concentrations between 0.5 and 5 mu m; at higher concentrations, APS may bind to the catalytic centers of ATP sulfurylase. Based on the assumption that cellular concentrations of APS fluctuate within this range, APS can therefore be regarded as a key modulator of PAPS synthase functions. The activation of the stable oxyanion sulfate via the formation of the sulfonucleotides adenosine-5'-phosphosulfate (APS) and 3'-phospho-adenosine-5'-phospho sulfate (PAPS) is vital for sulfur metabolism. Here we review the various inhibitory, regulatory and stabilising effects of APS and related nucleotides on sulfate-activating enzymes. For bifunctional PAPS synthases of metazoans, APS can be regarded as a key modulator of function.
The role of RNA interference (RNAi) in post-transcriptional regulation of complementary targets is well known. However, less is known about transcriptional silencing mechanisms mediated by RNAi. Such ...mechanisms have been characterized in yeast and plants, which suggests that similar RNA silencing mechanisms might operate in animals. A growing amount of experimental evidence indicates that short RNAs and their co-factor Argonaute proteins can regulate many nuclear processes in metazoans. PIWI-interacting RNAs (piRNAs) initiate transcriptional silencing of transposable elements, which leads to heterochromatin formation and/or DNA methylation. In addition, Argonaute proteins and short RNAs directly regulate Pol II transcription and splicing of euchromatic protein-coding genes and also affect genome architecture. Therefore, RNAi pathways can have a profound global impact on the transcriptional programs in cells during animal development. This article is part of a Special Issue entitled: Chromatin and epigenetic regulation of animal development.
Ca super(2+)/calmodulin dependent protein kinase II (CaMKII) is a broadly distributed metazoan Ser/Thr protein kinase that is important in neuronal and cardiac signaling. CaMKII forms oligomeric ...assemblies, typically dodecameric, in which the calcium-responsive kinase domains are organized around a central hub. We review the results of crystallographic analyses of CaMKII, including the recently determined structure of a full-length and autoinhibited form of the holoenzyme. These structures, when combined with other data, allow informed speculation about how CaMKII escapes calcium-dependence when calcium spikes exceed threshold frequencies.
Chen et al. (2014) described a suite of one-celled, Parapandorina-stage, Megaclonophycus-stage (some with dyads and tetrads), and matryoshka-stage fossils from the Doushantuo Formation, and ...interpreted them as representing a sequence of ontogenetic stages of the animal embryo-like fossil Megasphaera. Tang (2015) argues that the matryoshkas might have been parasites or symbionts, rather than developmental products of dyads and tetrads in Megaclonophycus-stage fossils. Assessing Tang's (2015) arguments against available evidence, we conclude that the matryoshkas likely represent an ontogenetic stage of Megasphaera. As such, they have the potential to illuminate the developmental biology, life cycle, and phylogenetic affinity of the enigmatic fossil Megasphaera.
Germ cells are the only cell type that passes genetic information to the next generation. In most metazoan species, primordial germ cells (PGCs) were induced from epiblasts by signals from the ...neighboring tissues. In vitro derivation of germ cells from the pluripotent stem cells (PSCs) such as embryonic stem cells (ESCs) and induced PSCs (iPSCs) are of great values for the treatment of infertility, for animal breeding, and for studying the mechanism of germ cell development. Although the derivations of male germ cells from PSCs have been previously reported, most of the studies failed to conduct the induction in a well-controlled and highly efficient manner. Here, we report the derivation of induced PGC-like cells (iPGCLCs) from mouse iPSCs via induced epiblast-like cells (iEpiLCs) as being monitored by the expression of enhanced green fluorescent protein gene under the control of the promoter of stimulated by retinoic acid 8 (Stra8-EGFP). The identity of iPGCLCs was characterized by examining the expression of multiple marker genes as well as by the recovery of spermatogenesis after they were transplanted to the testis of infertile W/W super(v) mice. Furthermore, iPGCLCs were either induced to germline stem cell-like cells (iGSCLCs) or reverted back to embryonic germ cell-like cells (iEGCLCs). In conclusion, we have established an efficient procedure for inducing iPSCs into iPGCLCs that can be further expanded and induced to more developed germ cells. This work indicates that the technology of in vitro germ cell induction is becoming more sophisticated and can be further improved.
Non-English title Sonnenschein, Carlos; Soto, Ana M
M.S. Médecine sciences,
06/2014, Volume:
30, Issue:
6-7
Journal Article
Peer reviewed
For almost a century, the somatic mutation theory (SMT) has been the prevalent theory to explain carcinogenesis. The SMT posits that the accumulation of mutations in the genome of a single normal ...cell is responsible for the transformation of such cell into a neoplasm. Implicitly, this theory claims that the default state of cells in metazoan is quiescence and that cancer is a cell-based, genetic and molecular disease. From lessons learned while performing our own research on control of cell proliferation and while adopting an organicist perspective, in 1999, the researchers proposed a competing theory, the tissue organization field theory (TOFT). In contraposition to the SMT, the TOFT posits that cancer is a tissue-based disease whereby carcinogens and mutations in the germ-line may alter normal interactions between the stroma and their adjacent epithelium. And the TOFT explicitly acknowledges that the default state of all cells is proliferation and motility, a premise that is relevant to and compatible with evolutionary theory.
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