Pediatric hypereosinophilic syndrome associated with liver damage, portal vein, splenic vein and superior mesenteric vein thromboses: a case report

BACKGROUND

The hypereosinophilic syndrome (HES) is a group of rare blood disorders characterized by persistent eosinophilia and damage to multiple organs. HES can be either primary, secondary or idiopathic. Secondary HES are commonly caused by parasitic infections, allergic reactions or cancer. We described a pediatric case of HES associated with liver damage and multiple thrombi. A 12-year-old boy with eosinophilia was complicated with severe thrombocytopenia, liver damage, portal vein, splenic vein, and superior mesenteric vein thromboses. The thrombi recanalized after treatment with methylprednisolone succinate and low molecular weight heparin. No side effects appeared after 1-month.

CONCLUSIONS

Corticosteroids should be used at an early stage of HES to prevent further damage to vital organs. Anticoagulants should be recommended only in cases with thrombosis which should be actively screened as a part of evaluation of end organ damage.

CCT2 is an aggrephagy receptor for clearance of solid protein aggregates

Protein aggregation is a hallmark of multiple human pathologies. Autophagy selectively degrades protein aggregates via aggrephagy. How selectivity is achieved has been elusive. Here, we identify the chaperonin subunit CCT2 as an autophagy receptor regulating the clearance of aggregation-prone proteins in the cell and the mouse brain. CCT2 associates with aggregation-prone proteins independent of cargo ubiquitination and interacts with autophagosome marker ATG8s through a non-classical VLIR motif. In addition, CCT2 regulates aggrephagy independently of the ubiquitin-binding receptors (P62, NBR1, and TAX1BP1) or chaperone-mediated autophagy. Unlike P62, NBR1, and TAX1BP1, which facilitate the clearance of protein condensates with liquidity, CCT2 specifically promotes the autophagic degradation of protein aggregates with little liquidity (solid aggregates). Furthermore, aggregation-prone protein accumulation induces the functional switch of CCT2 from a chaperone subunit to an autophagy receptor by promoting CCT2 monomer formation, which exposes the VLIR to ATG8s interaction and, therefore, enables the autophagic function.

A High-Quality Haplotype-Resolved Genome of Common Bermudagrass (Cynodon dactylon L.) Provides Insights Into Polyploid Genome Stability and Prostrate Growth

Common bermudagrass (Cynodon dactylon L.) is an important perennial warm-season turfgrass species with great economic value. However, the reference genome is still deficient in C. dactylon, which severely impedes basic studies and breeding studies. In this study, a high-quality haplotype-resolved genome of C. dactylon cultivar Yangjiang was successfully assembled using a combination of multiple sequencing strategies. The assembled genome is approximately 1.01 Gb in size and is comprised of 36 pseudo chromosomes belonging to four haplotypes. In total, 76,879 protein-coding genes and 529,092 repeat sequences were annotated in the assembled genome. Evolution analysis indicated that C. dactylon underwent two rounds of whole-genome duplication events, whereas syntenic and transcriptome analysis revealed that global subgenome dominance was absent among the four haplotypes. Genome-wide gene family analyses further indicated that homologous recombination-regulating genes and tiller-angle-regulating genes all showed an adaptive evolution in C. dactylon, providing insights into genome-scale regulation of polyploid genome stability and prostrate growth. These results not only facilitate a better understanding of the complex genome composition and unique plant architectural characteristics of common bermudagrass, but also offer a valuable resource for comparative genome analyses of turfgrasses and other plant species.

Human Ccr4 and Caf1 Deadenylases Regulate Proliferation and Tumorigenicity of Human Gastric Cancer Cells via Modulating Cell Cycle Progression

Simple Summary

Cancer cells generally reprogram their gene expression profiles to satisfy continuous growth, proliferation, and metastasis. Most eukaryotic mRNAs are degraded in a deadenylation-dependent pathway, in which deadenylases are the key enzymes. We found that human Ccr4 (hCcr4a/b) and Caf1 (hCaf1a/b), the dominant cytosolic deadenylases, were dysregulated in several types of cancers including stomach adenocarcinoma. Stably knocking down hCaf1a/b or hCcr4a/b blocks cell cycle progression by enhancing the levels of cell cycle inhibitors and by inhibiting the formation of processing bodies, which are cytosolic foci involved in mRNA metabolism. More importantly, depletion of hCaf1a/b or hCcr4a/b dramatically inhibits cell proliferation and tumorigenicity. Our results suggest that perturbating global RNA metabolism may provide a potential novel strategy for cancer treatment.

Abstract

Cancer cells generally have reprogrammed gene expression profiles to meet the requirements of survival, continuous division, and metastasis. An interesting question is whether the cancer cells will be affected by interfering their global RNA metabolism. In this research, we found that human Ccr4a/b (hCcr4a/b) and Caf1a/b (hCaf1a/b) deadenylases, the catalytic components of the Ccr4-Not complex, were dysregulated in several types of cancers including stomach adenocarcinoma. The impacts of the four deadenylases on cancer cell growth were studied by the establishment of four stable MKN28 cell lines with the knockdown of hCcr4a/b or hCaf1a/b or transient knockdown in several cell lines. Depletion of hCcr4a/b or hCaf1a/b significantly inhibited cell proliferation and tumorigenicity. Mechanistic studies indicated that the cells were arrested at the G2/M phase by knocking down hCaf1a, while arrested at the G0/G1 phase by depleting hCaf1b or hCcr4a/b. The four enzymes did not affect the levels of CDKs and cyclins but modulated the levels of CDK–cyclin inhibitors. We identified that hCcr4a/b, but not hCaf1a/b, targeted the p21 mRNA in the MKN28 cells. Furthermore, depletion of any one of the four deadenylases dramatically impaired processing-body formation in the MKN28 and HEK-293T cells. Our results highlight that perturbating global RNA metabolism may severely affect cancer cell proliferation, which provides a potential novel strategy for cancer treatment.

A novel F30S mutation in γS-crystallin causes autosomal dominant congenital nuclear cataract by increasing susceptibility to stresses

Despite of increasingly accumulated genetic variations of autosomal dominant congenital cataracts (ADCC), the causative genes of many ADCC patients remains unknown. In this research, we identified a novel F30S mutation in γS-crystallin from a three-generation Chinese family with ADCC. The patients possessing the F30S mutation exhibited nuclear cataract phenotype. The potential molecular mechanism underlying ADCC by the F30S mutation was investigated by comparing the structural features, stability and aggregatory potency of the mutated protein with the wild type protein. Spectroscopic experiments indicated that the F30S mutation did not affect γS-crystallin secondary structure compositions, but modified the microenvironments around aromatic side-chains. Thermal and chemical denaturation studies indicated that the mutation destabilized the protein and increased its aggregatory potency. The mutation altered the two-state unfolding of γS-crystallin to a three-state unfolding with the accumulation of an unfolding intermediate. The almost identical values in the changes of Gibbs free energies for transitions from the native state to intermediate and from the intermediate to unfolded state suggested that the mutation probably disrupted the cooperativity between the two domains during unfolding. Our results expand the genetic variation map of ADCC and provide novel insights into the molecular mechanism underlying ADCC caused by mutations in β/γ-crystallins.

Diverse functions of deadenylases in DNA damage response and genomic integrity

DNA damage response (DDR) is a coordinated network of diverse cellular processes including the detection, signaling, and repair of DNA lesions, the adjustment of metabolic network and cell fate determination. To deal with the unavoidable DNA damage caused by either endogenous or exogenous stresses, the cells need to reshape the gene expression profile to allow efficient transcription and translation of DDR-responsive messenger RNAs (mRNAs) and to repress the nonessential mRNAs. A predominant method to adjust RNA fate is achieved by modulating the 3'-end oligo(A) or poly(A) length via the opposing actions of polyadenylation and deadenylation. Poly(A)-specific ribonuclease (PARN) and the carbon catabolite repressor 4 (CCR4)-Not complex, the major executors of deadenylation, are indispensable to DDR and genomic integrity in eukaryotic cells. PARN modulates cell cycle progression by regulating the stabilities of mRNAs and microRNA (miRNAs) involved in the p53 pathway and contributes to genomic stability by affecting the biogenesis of noncoding RNAs including miRNAs and telomeric RNA. The CCR4-Not complex is involved in diverse pathways of DDR including transcriptional regulation, signaling pathways, mRNA stabilities, translation regulation, and protein degradation. The RNA targets of deadenylases are tuned by the DDR signaling pathways, while in turn the deadenylases can regulate the levels of DNA damage-responsive proteins. The mutual feedback between deadenylases and the DDR signaling pathways allows the cells to precisely control DDR by dynamically adjusting the levels of sensors and effectors of the DDR signaling pathways. Here, the diverse functions of deadenylases in DDR are summarized and the underlying mechanisms are proposed according to recent findings. This article is categorized under: RNA Processing > 3' End Processing RNA in Disease and Development > RNA in Disease RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms.

Semiholoenzyme optimizes activity and stability of a hyperthermostable iron-superoxide dismutase

Metal ion coordination is an essential step for the maturation of metalloenzymes. Generally, the metal coordination sites are thought to be fully occupied to achieve the maximum activity and stability. In this research, we compared the structural features, activity and stability of the apo-, semiholo- and holo-forms of a hyperthermostable tetrameric Fe-superoxide dismutase (SOD). Strikingly, the three forms of enzymes had similar compact tetrameric structures. Removal of iron ions destabilized subunit-subunit interactions during guanidine hydrochloride-induced unfolding. The partially metalized semiholoenzyme possessed most of the activity and identical hyperthermostability of the holoenzyme, but weaker propensity to aggregate. Furthermore, both of the iron content and activity of the semiholoenzyme were unaffected by a 200-fold excess iron ions in solutions, suggesting that conformation of the apo-subunits were forced to the close state by the iron-containing subunits. These observations suggest that fully metalized enzyme is probably nonessential for multimeric metalloenzymes and the semiholoenzyme may be a better choice. The unique properties of semiholoenzyme also provide the organisms a compromised solution to survival under metal deficiency conditions.

The Intrinsically Disordered C-Terminal Domain Triggers Nucleolar Localization and Function Switch of PARN in Response to DNA Damage

Poly(A)-specific ribonuclease (PARN), a multifunctional multi-domain deadenylase, is crucial to the regulation of mRNA turnover and the maturation of various non-coding RNAs. Despite extensive studies of the well-folding domains responsible for PARN catalysis, the structure and function of the C-terminal domain (CTD) remains elusive. PARN is a cytoplasm-nucleus shuttle protein with concentrated nucleolar distribution. Here, we identify the nuclear and nucleolar localization signals in the CTD of PARN. Spectroscopic studies indicated that PARN-CTD is intrinsically disordered with loosely packed local structures/tertiary structure. Phosphorylation-mimic mutation S557D disrupted the local structure and facilitated the binding of the CTD with the well-folded domains, with no impact on PARN deadenylase activity. Under normal conditions, the nucleolus-residing PARN recruited CBP80 into the nucleoli to repress its deadenylase activity, while DNA damage-induced phosphorylation of PARN-S557 expelled CBP80 from the nucleoli to discharge activity inhibition and attracted nucleoplasm-located CstF-50 into the nucleoli to activate deadenylation. The structure switch-induced function switch of PARN reshaped the profile of small nuclear non-coding RNAs to respond to DNA damage. Our findings highlight that the structure switch of the CTD induced by posttranslational modifications redefines the subset of binding partners, and thereby the RNA targets in the nucleoli.

Dissimilarity in the Contributions of the N-Terminal Domain Hydrophobic Core to the Structural Stability of Lens β/γ-Crystallins

Vertebrate lens β/γ-crystallins share a conserved tertiary structure consisting of four Greek-key motifs divided into two globular domains. Numerous inherited mutations in β/γ-crystallins have been linked to cataractogenesis. In this research, the folding mechanism underlying cataracts caused by the I21N mutation in βB2 was investigated by comparing the effect of mutagenesis on the structural features and stability of four β/γ-crystallins, βB1, βB2, γC, and γD. Our results showed that the four β/γ-crystallins differ greatly in solubility and stability against various stresses. The I21N mutation greatly impaired βB2 solubility and native structure as well as its stability against denaturation induced by guanidine hydrochloride, heat treatment, and ultraviolet irradiation. However, the deleterious effects were much weaker for mutations at the corresponding sites in βB1, γC, and γD. Molecular dynamics simulations indicated that the introduction of a nonnative hydrogen bond contributed to twisting Greek-key motif I outward, which might direct the misfolding of the I21N mutant of βB2. Meanwhile, partial hydration of the hydrophobic interior of the domain induced by the mutation destabilized βB1, γC, and γD. Our findings highlight the importance of nonnative hydrogen bond formation and hydrophobic core hydration in crystallin misfolding caused by inherited mutations.

Contributions of the C-terminal domain to poly(A)-specific ribonuclease (PARN) stability and self-association

Poly(A)-specific ribonuclease (PARN) catalyzes the degradation of mRNA poly(A) tail to regulate translation efficiency and mRNA decay in higher eukaryotic cells. The full-length PARN is a multi-domain protein containing the catalytic nuclease domain, the R3H domain, the RRM domain and the C-terminal intrinsically unstructured domain (CTD). The roles of the three well-structured RNA-binding domains have been extensively studied, while little is known about CTD. In this research, the impact of CTD on PARN stability and aggregatory potency was studied by comparing the thermal inactivation and denaturation behaviors of full-length PARN with two N-terminal fragments lacking CTD. Our results showed that K⁺ induced additional regular secondary structures and enhanced PARN stability against heat-induced inactivation, unfolding and aggregation. CTD prevented PARN from thermal inactivation but promoted thermal aggregation to initiate at a temperature much lower than that required for inactivation and unfolding. Blue-shift of Trp fluorescence during thermal transitions suggested that heat treatment induced rearrangements of domain organizations. CTD amplified the stabilizing effect of K⁺, implying the roles of CTD was mainly achieved by electrostatic interactions. These results suggested that CTD might dynamically interact with the main body of the molecule and release of CTD promoted self-association via electrostatic interactions.

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The C-terminal domain enhanced PARN stability against thermal inactivation.

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K⁺ reinforced the protective effect of the C-terminal domain.

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The C-terminal domain of PARN was intrinsically aggregation-prone.

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K⁺ modulated PARN self-association via the C-terminal domain.

Synthesis, Evaluation, and Structure-Activity Relationship Study of Lanosterol Derivatives To Reverse Mutant-Crystallin-Induced Protein Aggregation

We describe here the development of potent synthetic analogues of the naturally occurring triterpenoid lanosterol to reverse protein aggregation in cataracts. Lanosterol showed superiority to other scaffolds in terms of efficacy and generality in previous studies. Various modified lanosterol derivatives were synthesized via modification of the side chain, ring A, ring B, and ring C. Evaluation of these synthetic analogues draws a clear picture for SAR. In particular, hydroxylation of the 25-position in the side chain profoundly improved the potency, and 2-fluorination further enhanced the biological activity. This work also revealed that synthetic lanosterol analogues could reverse multiple types of mutant-crystallin aggregates in cell models with excellent potency and efficacy. Notably, lanosterol analogues have no cytotoxicity but can improve the viability of the HLE-B3 cell line. Furthermore, representative compound 6 successfully redissolved the aggregated crystallin proteins from the amyloid-like fibrils in a concentration-dependent manner.

Cataract-causing mutation S228P promotes βB1-crystallin aggregation and degradation by separating two interacting loops in C-terminal domain

β/γ-Crystallins are predominant structural proteins in the cytoplasm of lens fiber cells and share a similar fold composing of four Greek-key motifs divided into two domains. Numerous cataract-causing mutations have been identified in various β/γ-crystallins, but the mechanisms underlying cataract caused by most mutations remains uncharacterized. The S228P mutation in βB1-crystallin has been linked to autosomal dominant congenital nuclear cataract. Here we found that the S228P mutant was prone to aggregate and degrade in both of the human and E. coli cells. The intracellular S228P aggregates could be redissolved by lanosterol. The S228P mutation modified the refolding pathway of βB1-crystallin by affecting the formation of the dimeric intermediate but not the monomeric intermediate. Compared with native βB1-crystallin, the refolded S228P protein had less packed structures, unquenched Trp fluorophores and increased hydrophobic exposure. The refolded S228P protein was prone to aggregate at the physiological temperature and decreased the protective effect of βB1-crystallin on βA3-crystallin. Molecular dynamic simulation studies indicated that the mutation decreased the subunit binding energy and modified the distribution of surface electrostatic potentials. More importantly, the mutation separated two interacting loops in the C-terminal domain, which shielded the hydrophobic core from solvent in native βB1-crystallin. These two interacting loops are highly conserved in both of the N- and C-terminal domains of all β/γ-crystallins. We propose that these two interacting loops play an important role in the folding and structural stability of β/γ-crystallin domains by protecting the hydrophobic core from solvent access.

[Endometrioid carcinoma with sex cord-like formations and hyalinization of the uterine corpus: a clinicopathologic analysis of 5 cases]

OBJECTIVE

Endometrioid carcinoma with sex cord-like formations and hyalinization of the uterine corpus is a rare morphological variant of endometrioid carcinoma. The biphasic morphological features may cause confusion with carcinosarcoma of the uterus, leading to misdiagnosis. The aim of this article is to elucidate the clinicopathological characteristics of such endometrial carcinoma to avoid misdiagnosis.

METHODS

The clinical and pathological data of 5 cases of endometrioid carcinoma with sex cord-like formations and hyalinization of the uterine corpus were collected and analyzed.

RESULTS

The age of the 5 patients ranged from 29 to 39 years, with a mean age of 33 years. Four patients underwent surgery of radical hysterectomy, the other dilation and curettage biopsy. Among the former, 3 patients were at FIGO stageⅠA, the other ⅢC1. Microscopically, all 5 tumors contained endometrioid carcinoma components, 4 of which were FIGO gradeⅠ, the remaining one was grade Ⅱ. Each tumor was of variable proportions of corded and hyalinized areas ranging from 10% to 60%. The cells in the corded and hyalinized areas were epithelioid, fusiform and spindle in morphology, admixed with the endometrioid carcinoma component, resulting in a biphasic pattern. The corded and hyalinized component exhibited distinctively different immunophenotypical feature from that by the conventional endometrioid carcinoma component. The results of follow-up for 4 patients of 7 to 68 months (mean=26.5 months) revealed that all patients were alive without recurrence of the malignancy.

CONCLUSIONS

Endometrioid carcinoma with sex cord-like formations and hyalinization of the uterine corpus presents unique morphology, and the patients are usually young with relatively favorable prognosis. The definite mechanism for the pathogenesis of the sex cord-like formations and hyalinization needs further investigation.

An Intrinsically Disordered Motif Mediates Diverse Actions of Monomeric C-reactive Protein

Most proinflammatory actions of C-reactive protein (CRP) are only expressed following dissociation of its native pentameric assembly into monomeric form (mCRP). However, little is known about what underlies the greatly enhanced activities of mCRP. Here we show that a single sequence motif, i.e. cholesterol binding sequence (CBS; a.a. 35-47), is responsible for mediating the interactions of mCRP with diverse ligands. The binding of mCRP to lipoprotein component ApoB, to complement component C1q, to extracellular matrix components fibronectin and collagen, to blood coagulation component fibrinogen, and to membrane lipid component cholesterol, are all found to be markedly inhibited by the synthetic CBS peptide but not by other CRP sequences tested. Likewise, mutating CBS in mCRP also greatly impairs these interactions. Functional experiments further reveal that CBS peptide significantly reduces the effects of mCRP on activation of endothelial cells in vitro and on acute induction of IL-6 in mice. The potency and specificity of CBS are critically determined by the N-terminal residues Cys-36, Leu-37, and His-38; while the versatility of CBS appears to originate from its intrinsically disordered conformation polymorphism. Together, these data unexpectedly identify CBS as the major recognition site of mCRP and suggest that this motif may be exploited to tune the proinflammatory actions of mCRP.

A single residue substitution accounts for the significant difference in thermostability between two isoforms of human cytosolic creatine kinase

Creatine kinase (CK) helps maintain homeostasis of intracellular ATP level by catalyzing the reversible phosphotransfer between ATP and phosphocreatine. In humans, there are two cytosolic CK isoforms, the muscle-type (M) and the brain-type (B), which frequently function as homodimers (hMMCK and hBBCK). Interestingly, these isoenzymes exhibit significantly different thermostabilities, despite high similarity in amino acid sequences and tertiary structures. In order to investigate the mechanism of this phenomenon, in this work, we first used domain swapping and site-directed mutagenesis to search for the key residues responsible for the isoenzyme-specific thermostability. Strikingly, the difference in thermostability was found to principally arise from one single residue substitution at position 36 (Pro in hBBCK vs. Leu in hMMCK). We then engaged the molecular dynamics simulations to study the molecular mechanism. The calculations imply that the P36L substitution introduces additional local interactions around residue 36 and thus further stabilizes the dimer interface through a complex interaction network, which rationalizes the observation that hMMCK is more resistant to thermal inactivation than hBBCK. We finally confirmed this molecular explanation through thermal inactivation assays on Asp36 mutants that were proposed to devastate the local interactions and thus the dimer associations in both isoenzymes.

DsCaf1 is involved in environmental stress response of Dunaliella salina

Regulation of mRNA fates can alter the gene-expression profile promptly and specifically. Deadenylation is a process of which the poly(A) tail is degraded by deadenylases. By regulating mRNA turnover, deadenylases are involved in various vital cellular processes including stress responses. However, it is unclear whether deadenylases play a role in the adaption/tolerance of extremophiles. In this research, we cloned the deadenylase caf1 from Dunaliella salina (dscaf1), a unicellular green alga with exceptional halotolerance. In silicon analysis indicated that compared with the mesophilic alga Chlamydomonas reinhardtii caf1, dscaf1 promoter contained more elements responsive to abiotic stresses. Dscaf1 had an extremely high expression level under hypersaline conditions. When the D. salina cells were subject to stress shock, a two-stage response was observed for dscaf1 expression. The mRNA level of dscaf1 had an immediate 2-4 fold increase and followed by an ∼10 fold increase after hyperosmotic, heat or UV treatment, while had an about 3 fold increase quickly followed by an abrupt decrease after hypoosmotic or cold shock. The dissimilarity in dscaf1 expression patterns suggested that DsCaf1 is a stress-responsive deadenylase with the ability to regulate fates of a specific group of mRNAs for a certain type of stress.

RNAe: an effective method for targeted protein translation enhancement by artificial non-coding RNA with SINEB2 repeat

In this study, a universal protein expression enhancement RNA tool, termed RNAe, was developed by modifying a recently discovered natural long non-coding RNA. At the moment, RNAe is the only technology for gene expression enhancement, as opposed to silencing, at the post-transcriptional level. With this technology, an expression enhancement of 50–1000% is achievable, with more than 200% enhancement achieved in most cases. This work identified the sufficient and necessary element for RNAe function, which was found to be merely 300 nucleotides long and was named minRNAe. It contains a 72-nt 5' pairing sequence which determines the specificity, a 167-nt short non-pairing interspersed nuclear element (SINE) B2 sequence which enhances ribosome recruitment to the target mRNA, and a poly(A) tail, provided together on a plasmid bearing the appropriate sequences. Cellular delivery of RNAe was achieved using routine transfection. The RNAe platform was validated in several widely-used mammalian cell lines. It was proven to be efficient and flexible in specifically enhancing the expression of various endogenous and exogenous proteins of diverse functions in a dose-dependent manner. Compared to the expression-inhibitory tool RNAi, the RNAe tool has a comparable effect size, with an enhancing as opposed to inhibitory effect. One may predict that this brand new technology for enhancing the production of proteins will find wide applications in both research and biopharmaceutical production.

Dunaliella salina Hsp90 is halotolerant

Dunaliella salina is a unicellular green alga with exceptional halotolerance. Although the D. salina cells are capable to proliferate in hypersaline medium, the intracellular salt concentrations are maintained at a low level. Thus the extracellular but not intracellular Dunaliella proteins are expected to be highly halotolerant. In this research, we compared the salt-dependence of the activity and stability of Hsp90s from the halotolerant alga D. salina (dsHsp90) and the mesophilic alga Chlamydomonas reinhardtii (crHsp90). We found that the ATPase activity of crHsp90 could be enhanced about six-fold by 2M NaCl, while the activity of dsHsp90 showed a much weaker dependence on salinity. When denatured by urea, both crHsp90 and dsHsp90 exhibited an apparent three-state unfolding with the population of an unfolding intermediate. High salinity significantly decreased the Gibbs free energy change of crHsp90 but not dsHsp90 for the transition from the native state to the intermediate. The little dependence of dsHsp90 activity and folding on salinity suggests that dsHsp90 is halotolerant though it is an intracellular protein. We propose that the halotolerance of intracellular Dunaliella proteins might play a role in fighting against the transient intracellular salt fluctuations during hyperosmotic or hypoosmotic shock.

Depletion of poly(A)-specific ribonuclease (PARN) inhibits proliferation of human gastric cancer cells by blocking cell cycle progression

Regulation of mRNA decay plays a crucial role in the post-transcriptional control of cell growth, survival, differentiation, death and senescence. Deadenylation is a rate-limiting step in the silence and degradation of the bulk of highly regulated mRNAs. However, the physiological functions of various deadenylases have not been fully deciphered. In this research, we found that poly(A)-specific ribonuclease (PARN) was upregulated in gastric tumor tissues and gastric cancer cell lines MKN28 and AGS. The cellular function of PARN was investigated by stably knocking down the endogenous PARN in the MKN28 and AGS cells. Our results showed that PARN-depletion significantly inhibited the proliferation of the two types of gastric cancer cells and promoted cell death, but did not significantly affect cell motility and invasion. The depletion of PARN arrested the gastric cancer cells at the G0/G1 phase by upregulating the expression levels of p53 and p21 but not p27. The mRNA stability of p53 was unaffected by PARN-knockdown in both types of cells. A significant stabilizing effect of PARN-depletion on p21 mRNA was observed in the AGS cells but not in the MKN28 cells. We further showed that the p21 3'-UTR triggered the action of PARN in the AGS cells. The dissimilar observations between the MKN28 and AGS cells as well as various stress conditions suggested that the action of PARN strongly relied on protein expression profiles of the cells, which led to heterogeneity in the stability of PARN-targeted mRNAs.

Formation of high-order oligomers by a hyperthemostable Fe-superoxide dismutase (tcSOD)

Hyperthermostable proteins are highly resistant to various extreme conditions. Many factors have been proposed to contribute to their ultrahigh structural stability. Some thermostable proteins have larger oligomeric size when compared to their mesophilic homologues. The formation of compact oligomers can minimize the solvent accessible surface area and increase the changes of Gibbs free energy for unfolding. Similar to mesophilic proteins, hyperthermostable proteins also face the problem of unproductive aggregation. In this research, we investigated the role of high-order oligomerization in the fight against aggregation by a hyperthermostable superoxide dismutase identified from Tengchong, China (tcSOD). Besides the predominant tetramers, tcSOD could also form active high-order oligomers containing at least eight subunits. The dynamic equilibrium between tetramers and high-order oligomers was not significantly affected by pH, salt concentration or moderate temperature. The secondary and tertiary structures of tcSOD remained unchanged during heating, while cross-linking experiments showed that there were conformational changes or structural fluctuations at high temperatures. Mutational analysis indicated that the last helix at the C-terminus was involved in the formation of high-order oligomers, probably via domain swapping. Based on these results, we proposed that the reversible conversion between the active tetramers and high-order oligomers might provide a buffering system for tcSOD to fight against the irreversible protein aggregation pathway. The formation of active high-order oligomers not only increases the energy barrier between the native state and unfolded/aggregated state, but also provides the enzyme the ability to reproduce the predominant oligomers from the active high-order oligomers.

Self-association of poly(A)-specific ribonuclease (PARN) triggered by the R3H domain

Poly(A)-specific ribonuclease (PARN) is a deadenylase with three RNA-binding domains (the nuclease, R3H and RRM domains) and a C-terminal domain. PARN participates in diverse physiological processes by regulating mRNA fates through deadenylation. PARN mainly exists as a dimer in dilute solutions. In this research, we found that PARN could self-associate into tetramer and high-order oligomers both in vitro and in living cells. Mutational and spectroscopic analysis indicated that PARN oligomerization was triggered by the R3H domain, which led to the solvent-exposed Trp219 fluorophore to become buried in a solvent-inaccessible microenvironment. The RRM and C-terminal domains also played a role in modulating the dissociation rate of the tetrameric PARN. Enzymatic analysis indicated that tetramerization did not affect the catalytic behavior of the full-length PARN and truncated enzymes containing the RRM domain, which might be caused by the high propensity of the dimeric proteins to self-associate into oligomers. Tetramerization significantly enhanced the catalytic activity and processivity of the truncated form with the removal of the RRM and C-terminal domains. The results herein suggested that self-association might be one of the regulation methods for PARN to achieve a highly regulated deadenylase activity. We propose that self-association may facilitate PARN to concentrate around the target mRNAs by restricted diffusion.

The N-terminal extension of βB1-crystallin chaperones β-crystallin folding and cooperates with αA-crystallin

β/γ-Crystallins are the major structural proteins in mammalian lens. The N-terminal truncation of βB1-crystallin has been associated with the regulation of β-crystallin size distributions in human lens. Herein we studied the roles of βB1 N-terminal extension in protein structure and folding by constructing five N-terminal truncated forms. The truncations did not affect the secondary and tertiary structures of the main body as well as stability against denaturation. Truncations with more than 28 residues off the N-terminus promoted the dissociation of the dimeric βB1 into monomers in diluted solutions. Interestingly, the N-terminal extension facilitated βB1 to adopt the correct folding pathway, while truncated proteins were prone to undergo the misfolding/aggregation pathway during kinetic refolding. The N-terminal extension of βB1 acted as an intramolecular chaperone (IMC) to regulate the kinetic partitioning between folding and misfolding. The IMC function of the N-terminal extension was also critical to the correct refolding of β-crystallin heteromer and the action of the lens-specific molecular chaperone αA-crystallin. The cooperation between IMC and molecular chaperones produced a much stronger chaperoning effect than if they acted separately. To our knowledge, this is the first report showing the cooperation between IMC and molecular chaperones.

Deadenylation: enzymes, regulation, and functional implications

Lengths of the eukaryotic messenger RNA (mRNA) poly(A) tails are dynamically changed by the opposing effects of poly(A) polymerases and deadenylases. Modulating poly(A) tail length provides a highly regulated means to control almost every stage of mRNA lifecycle including transcription, processing, quality control, transport, translation, silence, and decay. The existence of diverse deadenylases with distinct properties highlights the importance of regulating poly(A) tail length in cellular functions. The deadenylation activity can be modulated by subcellular locations of the deadenylases, cis-acting elements in the target mRNAs, trans-acting RNA-binding proteins, posttranslational modifications of deadenylase and associated factors, as well as transcriptional and posttranscriptional regulation of the deadenylase genes. Among these regulators, the physiological functions of deadenylases are largely dependent on the interactions with the trans-acting RNA-binding proteins, which recruit deadenylases to the target mRNAs. The task of these RNA-binding proteins is to find and mark the target mRNAs based on their sequence features. Regulation of the regulators can switch on or switch off deadenylation and thereby destabilize or stabilize the targeted mRNAs, respectively. The distinct domain compositions and cofactors provide various deadenylases the structural basis for the recruitments by distinct RNA-binding protein subsets to meet dissimilar cellular demands. The diverse deadenylases, the numerous types of regulators, and the reversible posttranslational modifications together make up a complicated network to precisely regulate intracellular mRNA homeostasis. This review will focus on the diverse regulators of various deadenylases and will discuss their functional implications, remaining problems, and future challenges.

Knockdown of creatine kinase B inhibits ovarian cancer progression by decreasing glycolysis

Creatine kinase plays a key role in the energy homeostasis of vertebrate cells. Creatine kinase B (CKB), a cytosolic isoform of creatine kinase, shows upregulated expression in a variety of cancers. In this research, we confirmed that some ovarian cancer tissues had elevated CKB expression at the protein level. The functions of CKB in ovarian cancer progression were investigated in the ovarian cancer cell line Skov3, which has a high CKB expression. It was found that CKB knockdown inhibited Skov3 cell proliferation and induced apoptosis under hypoxia or hypoglycemia conditions. CKB depletion also sensitized Skov3 to chemotherapeutic agents. Furthermore, the CKB knockdown reduced glucose consumption and lactate production, and increased ROS production and oxygen consumption. This suggested that CKB knockdown decreased cytosolic glycolysis and resulted in a tumor suppressive metabolic state in Skov3 cells. Consequently, we found that the knockdown of CKB induced G2 arrest in cell cycle by elevating p21 expression and affected the PI3K/Akt and AMPK pathways. These findings provide new insights in the role of CKB in cancer cell survival and tumor progression. Our results also suggest that CKB depletion/inhibition in combination with chemotherapeutic agents might have synergistic effects in ovarian cancer therapy.

Distinct roles of the R3H and RRM domains in poly(A)-specific ribonuclease structural integrity and catalysis

Deadenylases specifically catalyze the degradation of eukaryotic mRNA poly(A) tail in the 3'- to 5'-end direction with the release of 5'-AMP as the product. Among the deadenylase family, poly(A)-specific ribonuclease (PARN) is unique in its domain composition, which contains three potential RNA-binding domains: the catalytic nuclease domain, the R3H domain and the RRM domain. In this research, we investigated the roles of these RNA-binding domains by comparing the structural features and enzymatic properties of mutants lacking either one or two of the three RNA-binding domains. The results showed that the R3H domain had the ability to bind various oligonucleotides at the micromolar level with no oligo(A) specificity. The removal of the R3H domain dissociated PARN into monomers, which still possessed the RNA-binding ability and catalytic functions. Unlike the critical role of the RRM domain in PARN processivity, the removal of the R3H domain did not affect the catalytic pattern of PARN. Our results suggested that both R3H and RRM domains were essential for the high affinity of long poly(A) substrate, but the R3H domain did not contribute to the substrate recognition of PARN. Compared to the RRM domain, the R3H domain played a more important role in the structural integrity of the dimeric PARN. The multiple RNA-binding domain architecture endows PARN the property of highly efficient catalysis in a highly processive mode.

Chaperone-like effect of the linker on the isolated C-terminal domain of rabbit muscle creatine kinase

Intramolecular chaperones (IMCs), which are specific domains/segments encoded in the primary structure of proteins, exhibit chaperone-like activity against the aggregation of the other domains in the same molecule. In this research, we found that the truncation of the linker greatly promoted the thermal aggregation of the isolated C-terminal domain (CTD) of rabbit muscle creatine kinase (RMCK). Either the existence of the linker covalently linked to CTD or the supply of the synthetic linker peptide additionally could successfully protect the CTD of RMCK against aggregation in a concentration-dependent manner. Truncated fragments of the linker also behaved as a chaperone-like effect with lower efficiency, revealing the importance of its C-terminal half in the IMC function of the linker. The aggregation sites in the CTD of RMCK were identified by molecular dynamics simulations. Mutational analysis of the three key hydrophobic residues resulted in opposing effects on the thermal aggregation between the CTD with intact or partial linker, confirming the role of linker as a lid to protect the hydrophobic residues against exposure to solvent. These observations suggested that the linkers in multidomain proteins could act as IMCs to facilitate the correct folding of the aggregation-prone domains. Furthermore, the intactness of the IMC linker after proteolysis modulates the production of off-pathway aggregates, which may be important to the onset of some diseases caused by the toxic effects of aggregated proteolytic fragments.

The congenital cataract-linked A2V mutation impairs tetramer formation and promotes aggregation of βB2-crystallin

β/γ-Crystallins, the major structural proteins in human lens, are highly conserved in their tertiary structures but distinct in the quaternary structures. The N- and C-terminal extensions have been proposed to play a crucial role in mediating the size of β-crystallin assembly. In this research, we investigated the molecular mechanism underlying the congenital hereditary cataract caused by the recently characterized A2V mutation in βB2-crystallin. Spectroscopic experiments indicated that the mutation did not affect the secondary and tertiary structures of βB2-crystallin. The mutation did not affect the formation of βB2/βA3-crystallin heteromer as well as the stability and folding of the heteromer, suggesting that the mutation might not interfere with the protein interacting network in the lens. However, the tetramerization of βB2-crystallin at high protein concentrations was retarded by the A2V mutation. The mutation slightly decreased the thermal stability and promoted the thermal aggregation of βB2-crystallin. Although it did not influence the stability of βB2-crystallin against denaturation induced by chemical denaturants and UV irradiation, the A2V mutant was more prone to be trapped in the off-pathway aggregation process during kinetic refolding. Our results suggested that the A2V mutation might lead to injury of lens optical properties by decreasing βB2-crystallin stability against heat treatment and by impairing βB2-crystallin assembly into high-order homo-oligomers.

The N-terminus modulates human Caf1 activity, structural stability and aggregation

Caf1 is a deadenylase component of the CCR4-Not complex. Here we found that the removal of the N-terminus resulted in a 30% decrease in human Caf1 (hCaf1) activity, but had no significant influence on main domain structure. The removal of the N-terminus led to a decrease in the thermal stability, while the existence of the N-terminus promoted hCaf1 thermal aggregation. Homology modeling indicated that the N-terminus had a potency to form a short α-helix interacted with the main domain. Thus the N-terminus played a role in modulating hCaf1 activity, stability and aggregation.

Two distinct states of Escherichia coli cells that overexpress recombinant heterogeneous β-galactosidase

The mechanism by which inclusion bodies form is still not well understood, partly because the dynamic processes of the inclusion body formation and its solubilization have hardly been investigated at an individual cell level, and so the important detailed information has not been acquired for the mechanism. In this study, we investigated the in vivo folding and aggregation of Aspergillus phoenicis β-D-galactosidase fused to a red fluorescence protein in individual Escherichia coli cells. The folding status and expression level of the recombinant β-D-galactosidase at an individual cell level was analyzed by flow cytometry in combination with transmission electron microscopy and Western blotting. We found that individual E. coli cells fell into two distinct states, one containing only inclusion bodies accompanied with low galactosidase activity and the other containing the recombinant soluble galactosidase accompanied with high galactosidase activity. The majority of the E. coli cells in the later state possessed no inclusion bodies. The two states of the cells were shifted to a cell state with high enzyme activity by culturing the cells in isopropyl 1-thio-β-D-galactopyranoside-free medium after an initial protein expression induction in isopropyl 1-thio-β-D-galactopyranoside-containing medium. This shift of the cell population status took place without the level change of the β-D-galactosidase protein in individual cells, indicating that the factor(s) besides the crowdedness of the recombinant protein play a major role in the cell state transition. These results shed new light on the mechanism of inclusion body formation and will facilitate the development of new strategies in improving recombinant protein quality.

A novel CRYGD mutation (p.Trp43Arg) causing autosomal dominant congenital cataract in a Chinese family

To identify the genetic defect associated with autosomal dominant congenital nuclear cataract in a Chinese family, molecular genetic investigation via haplotype analysis and direct sequencing were performed Sequencing of the CRYGD gene revealed a c.127T>C transition, which resulted in a substitution of a highly conserved tryptophan with arginine at codon 43 (p.Trp43Arg). This mutation co-segregated with all affected individuals and was not observed in either unaffected family members or in 200 normal unrelated individuals. Biophysical studies indicated that the p.Trp43Arg mutation resulted in significant tertiary structural changes. The mutant protein was much less stable than the wild-type protein, and was more prone to aggregate when subjected to environmental stresses such as heat and UV irradiation. © 2010 Wiley-Liss, Inc.

The congenital cataract-linked G61C mutation destabilizes γD-crystallin and promotes non-native aggregation

γD-crystallin is one of the major structural proteins in human eye lens. The solubility and stability of γD-crystallin play a crucial role in maintaining the optical properties of the lens during the life span of an individual. Previous study has shown that the inherited mutation G61C results in autosomal dominant congenital cataract. In this research, we studied the effects of the G61C mutation on γD-crystallin structure, stability and aggregation via biophysical methods. CD, intrinsic and extrinsic fluorescence spectroscopy indicated that the G61C mutation did not affect the native structure of γD-crystallin. The stability of γD-crystallin against heat- or GdnHCl-induced denaturation was significantly decreased by the mutation, while no influence was observed on the acid-induced unfolding. The mutation mainly affected the transition from the native state to the intermediate but not that from the intermediate to the unfolded or aggregated states. At high temperatures, both proteins were able to form aggregates, and the aggregation of the mutant was much more serious than the wild type protein at the same temperature. At body temperature and acidic conditions, the mutant was more prone to form amyloid-like fibrils. The aggregation-prone property of the mutant was not altered by the addition of reductive reagent. These results suggested that the decrease in protein stability followed by aggregation-prone property might be the major cause in the hereditary cataract induced by the G61C mutation.

A novel mutation in CRYBB1 associated with congenital cataract-microcornea syndrome: the p.Ser129Arg mutation destabilizes the βB1/βA3-crystallin heteromer but not the βB1-crystallin homomer

Congenital cataract-microcornea syndrome (CCMC) is a clinically and genetically heterogeneous condition characterized by lens opacities and microcornea. It appears as a distinct phenotype of heritable congenital cataract. Here we report a large Chinese family with autosomal dominant congenital cataract and microcornea. Evidence for linkage was detected at marker D22S1167 (LOD score [Z]=4.49, recombination fraction [θ]=0.0), which closely flanks the â-crystallin gene cluster locus. Direct sequencing of the candidate âB1-crystallin gene (CRYBB1) revealed a c.387C>A transversion in exon 4, which cosegregated with the disease in the family and resulted in the substitution of serine by arginine at codon 129 (p.Ser129Arg). A comparison of the biophysical properties of the recombinant β-crystallins revealed that the mutation impaired the structures of both βB1-crystallin homomer and βB1/βA3-crystallin heteromer. More importantly, the mutation significantly decreased the thermal stability of βB1/βA3-crystallin but not βB1-crystallin. These findings highlight the importance of protein-protein interactions among β-crystallins in maintaining lens transparency, and provide a novel insight into the molecular mechanism underlying the pathogenesis of human CCMC. © 2011 Wiley-Liss, Inc.

Dissecting the key residues crucial for the species-specific thermostability of muscle-type creatine kinase

Species-specific protein thermal stability is closely correlated to the living conditions of the organism, especially to its body temperature. In this research, human and zebrafish muscle-type creatine kinases (MMCKs) were taken as model proteins to investigate the molecular adaptation of proteins in poikilothermal and homoiothermal animals. Both the optimal temperature for catalysis and the thermal stability of human MMCK was much higher than those of zebrafish MMCK. Sequence alignment identified 9 amino acid variations conserved in either the teleost MMCKs or the mammal and electric ray MMCKs. Bidirectional mutations were performed to find the residues with beneficial mutations. The results showed that two residues close to the dimer interface of MMCK, the 46th and 146th residue, were crucial for species-specific thermal stability.

Effects of acrylamide on the activity and structure of human brain creatine kinase

Acrylamide is widely used worldwide in industry and it can also be produced by the cooking and processing of foods. It is harmful to human beings, and human brain CK (HBCK) has been proposed to be one of the important targets of acrylamide. In this research, we studied the effects of acrylamide on HBCK activity, structure and the potential binding sites. Compared to CKs from rabbit, HBCK was fully inactivated at several-fold lower concentrations of acrylamide, and exhibited distinct properties upon acrylamide-induced inactivation and structural changes. The binding sites of acrylamide were located at the cleft between the N- and C-terminal domains of CK, and Glu232 was one of the key binding residues. The effects of acrylamide on CK were proposed to be isoenzyme- and species-specific, and the underlying molecular mechanisms were discussed.

Conformational stability and multistate unfolding of poly(A)-specific ribonuclease

Poly(A)-specific ribonuclease (PARN) specifically catalyzes the degradation of the poly(A) tails of single-stranded mRNAs in a highly processive mode. PARN participates in diverse and important intracellular processes by acting as a regulator of mRNA stability and translational efficiency. In this article, the equilibrium unfolding of PARN was studied using both guanidine hydrochloride and urea as chemical denaturants. The unfolding of PARN was characterized as a multistate process, but involving dissimilar equilibrium intermediates when denatured by the two denaturants. A comparison of the spectral characteristics of these intermediates indicated that the conformational changes at low concentrations of the chemical denaturants were more likely to be rearrangements of the tertiary and quaternary structures. In particular, an inactive molten globule-like intermediate was identified to exist as soluble non-native oligomers, and the formation of the oligomers was modulated by electrostatic interactions. An active dimeric intermediate unique to urea-induced unfolding was characterized to have increased regular secondary structures and modified tertiary structures, implying that additional regular structures could be induced by environmental stresses. The dissimilarity in the unfolding pathways induced by guanidine hydrochloride and urea suggest that electrostatic interactions play an important role in PARN stability and regulation. The appearance of multiple intermediates with distinct properties provides the structural basis for the multilevel regulation of PARN by conformational changes.