Functional implications of CaMKII alternative splicing Sloutsky, Roman; Stratton, Margaret M.
European journal of neuroscience/EJN. European journal of neuroscience,
October 2021, Letnik:
54, Številka:
8
Journal Article
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Ca2+/calmodulin‐dependent protein kinase II (CaMKII) is known to be a crucial regulator in the post‐synapse during long‐term potentiation. This important protein has been the subject of many studies ...centered on understanding memory at the molecular, cellular, and organismic level. CaMKII is encoded by four genes in humans, all of which undergo alternative splicing at the RNA level, leading to an enormous diversity of expressed proteins. Advances in sequencing technologies have facilitated the discovery of many new CaMKII transcripts. To date, newly discovered CaMKII transcripts have been incorporated into an ambiguous naming scheme. Herein, we review the initial experiments leading to the discovery of CaMKII and its subsequent variants. We propose the adoption of a new, unambiguous naming scheme for CaMKII variants. Finally, we discuss biological implications for CaMKII splice variants.
Alternative splicing produces a diverse range of linkers connecting CaMKII kinase domains to the central holoenzyme hub. We review the exon architecture and splicing rules of CaMKII genes, the 40‐year history of the discovery of CaMKII and its splice variants, and the structural and functional implications of alternative splicing of CaMKII transcripts. Finally, we propose a systematic splice variant naming scheme aimed to resolve decades of confusion in CaMKII variant nomenclature.
Reactivation of a silent transcriptional program is a critical step in successful axon regeneration following injury. Yet how such a program is unlocked after injury remains largely unexplored. We ...found that axon injury in peripheral sensory neurons elicits a back-propagating calcium wave that invades the soma and causes nuclear export of HDAC5 in a PKCμ-dependent manner. Injury-induced HDAC5 nuclear export enhances histone acetylation to activate a proregenerative gene-expression program. HDAC5 nuclear export is required for axon regeneration, as expression of a nuclear-trapped HDAC5 mutant prevents axon regeneration, whereas enhancing HDAC5 nuclear export promotes axon regeneration in vitro and in vivo. Components of this HDAC5 pathway failed to be activated in a model of central nervous system injury. These studies reveal a signaling mechanism from the axon injury site to the soma that controls neuronal growth competence and suggest a role for HDAC5 as a transcriptional switch controlling axon regeneration.
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•A back-propagating calcium wave causes HDAC5 nuclear export in injured neurons•HDAC5 nuclear export leads to increased histone acetylation•HDAC5 nuclear export activates a proregenerative gene-expression program•Promoting HDAC5 nuclear export accelerates axon regeneration
Axon injury promotes nuclear export of the histone deacetylase HDAC5. The resulting increase in histone acetylation acts as an epigenetic switch that activates the axon regeneration program.
Evolutionary reconstruction algorithms produce models of the evolutionary history of proteins or species. Such algorithms are highly sensitive to their inputs: the sequences used and their ...alignments. Here, we asked whether the variance introduced by selecting different input sequences could be used to better identify accurate evolutionary models. We subsampled from available ortholog sequences and measured the distribution of observed relationships between paralogs produced across hundreds of models inferred from the subsamples. We observed two important phenomena. First, the reproducibility of an all-sequence, single-alignment reconstruction, measured by comparing topologies inferred from 90% subsamples, directly correlates with the accuracy of that single-alignment reconstruction, producing a measurable value for something that has been traditionally unknowable. Second, topologies that are most consistent with the observations made in the ensemble are more accurate and we present a meta algorithm that exploits this property to improve model accuracy.
Since the advent of large-scale genomic sequencing, and the consequent availability of large numbers of homologous protein sequences, there has been burgeoning development of methods for extracting ...functional information from multiple sequence alignments (MSAs). One type of analysis seeks to identify specificity determining positions (SDPs) based on the assumption that such positions are highly conserved within groups of sequences sharing functional specificity, but conserved to different amino acids in different specificity groups. This unsupervised approach to utilizing evolutionary information may elucidate mechanisms of specificity in protein-protein interactions, catalytic activity of enzymes, sensitivity to allosteric regulation, and other types of protein functionality. We present an analysis of SDPs in the LacI family of transcriptional regulators in which we 1) relax the constraint that all specificity groups must contribute to SDP signal, and 2) use a novel approach to robust treatment of sequence alignment uncertainty based on sub-sampling. We find that the vast majority of SDP signal occurs at positions with a conservation pattern that significantly complicates detection by previously described methods. This pattern, which we term "partial SDP", consists of the commonly accepted SDP conservation pattern among a subset of specificity groups and strong degeneracy among the rest. An upshot of this fact is that the SDP complement of every specificity group appears to be unique. Additionally, sub-sampling gives us the ability to assign a confidence interval to the SDP score, as well as increase fidelity, as compared to analysis of a single, comprehensive alignment-the current standard in multiple sequence alignment methodologies.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Ca2+/calmodulin-dependent protein kinase II (CaMKII) is a signaling protein required for long-term memory. When activated by Ca2+/CaM, it sustains activity even after the Ca2+ dissipates. In addition ...to the well-known autophosphorylation-mediated mechanism, interaction with specific binding partners also persistently activates CaMKII. A long-standing model invokes two distinct S and T sites. If an interactor binds at the T-site, then it will preclude autoinhibition and allow substrates to be phosphorylated at the S site. Here, we specifically test this model with X-ray crystallography, molecular dynamics simulations, and biochemistry. Our data are inconsistent with this model. Co-crystal structures of four different activators or substrates show that they all bind to a single continuous site across the kinase domain. We propose a mechanistic model where persistent CaMKII activity is facilitated by high-affinity binding partners that kinetically compete with autoinhibition by the regulatory segment to allow substrate phosphorylation.
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•CaMKII kinase domain binds all interactors through a single continuous binding site•A salt bridge interaction far from active site increases binding affinity•αD helix changes conformation between autoinhibited and active “on” states•High-affinity binders may prolong activation by maintaining the “on” state
Özden et al. report high-resolution structures of CaMKII bound to peptides from proteins that are crucial for memory. All interactors dock onto the same single binding site using conserved interactions. A model is proposed for how high-affinity interactors prolong CaMKII activity by competing with autoinhibition.
RRM, or RNA-recognition motif, domains are the largest class of single-stranded RNA binding domains in the human proteome and play important roles in RNA processing, splicing, export, stability, ...packaging, and degradation. Using a current database of post-translational modifications (PTMs), ProteomeScout, we found that RRM domains are also one of the most heavily modified domains in the human proteome. Here, we present two interesting findings about RRM domain modifications, found by mapping known PTMs onto RRM domain alignments and structures. First, we find significant overlap of ubiquitination and acetylation within RRM domains, suggesting the possibility for ubiquitination-acetylation crosstalk. Additionally, an analysis of quantitative study of ubiquitination changes in response to proteasome inhibition highlights the uniqueness of RRM domain ubiquitination – RRM domain ubiquitination decreases in response to proteasome inhibition, whereas the majority of sites increase. Second, we found conservation of tyrosine phosphorylation within the RNP1 and RNP2 consensus sequences, which coordinate RNA binding – suggesting a possible role for regulation of RNA binding by tyrosine kinase signaling. These observations suggest there are unique regulatory mechanisms of RRM function that have yet to be uncovered and that the RRM domain represents a model system for further studies on understanding PTM crosstalk.
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•RNA-recognition motif (RRM) domains are one of the most heavily modified domains in the human proteome.•Acetylation and ubiquitination are conserved within the same positions of RRM domain alignments.•Unlike most ubiquitination sites, RRM domain sites decrease when the proteasome is inhibited, corresponding with high degrees of acetylation and suggesting significant PTM crosstalk.•Tyrosine phosphorylation is also conserved and falls within the regions known to interact with RNA, suggesting that RNA binding is regulated by tyrosine phosphorylation.
Calcium/calmodulin-dependent protein kinase II (CaMKII) plays a central role in Ca
signaling throughout the body. In the hippocampus, CaMKII is required for learning and memory. Vertebrate genomes ...encode four CaMKII homologs: CaMKIIα, CaMKIIβ, CaMKIIγ, and CaMKIIδ. All CaMKIIs consist of a kinase domain, a regulatory segment, a variable linker region, and a hub domain, which is responsible for oligomerization. The four proteins differ primarily in linker length and composition because of extensive alternative splicing. Here, we report the heterogeneity of CaMKII transcripts in three complex samples of human hippocampus using deep sequencing. We showed that hippocampal cells contain a diverse collection of over 70 CaMKII transcripts from all four CaMKII-encoding genes. We characterized the Ca
/CaM sensitivity of hippocampal CaMKII variants spanning a broad range of linker lengths and compositions. The effect of the variable linker on Ca
/CaM sensitivity depended on the kinase and hub domains. Moreover, we revealed a previously uncharacterized role for the hub domain as an allosteric regulator of kinase activity, which may provide a pharmacological target for modulating CaMKII activity. Using small-angle x-ray scattering and single-particle cryo-electron microscopy (cryo-EM), we present evidence for extensive interactions between the kinase and the hub domains, even in the presence of a 30-residue linker. Together, these data suggest that Ca
/CaM sensitivity in CaMKII is homolog dependent and includes substantial contributions from the hub domain. Our sequencing approach, combined with biochemistry, provides insights into understanding the complex pool of endogenous CaMKII splice variants.
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