Cooperative function of the CHD5-like protein Mdm39p with a P-type ATPase Spf1p in the maintenance of ER homeostasis in Saccharomyces cerevisiae

The structure and function of P5A-ATPases

Endoplasmic reticulum (ER) membrane resident P5A-ATPases broadly affect protein biogenesis and quality control, and yet their molecular function remains debated. Here, we report cryo-EM structures of a P5A-ATPase, CtSpf1, covering multiple transport intermediates of the E1 → E1-ATP → E1P-ADP → E1P → E2P → E2.Pi → E2 → E1 cycle. In the E2P and E2.Pi states a cleft spans the entire membrane, holding a polypeptide cargo molecule. The cargo includes an ER luminal extension, pinpointed as the C-terminus in the E2.Pi state, which reenters the membrane in E2P. The E1 structure harbors a cytosol-facing cavity that is blocked by an insertion we refer to as the Plug-domain. The Plug-domain is nestled to key ATPase features and is displaced in the E1P-ADP and E1P states. Collectively, our findings are compatible with a broad range of proteins as cargo, with the P5A-ATPases serving a role in membrane removal of helices, although insertion/secretion cannot be excluded, as well as with a mechanistic role of the Plug-domain.

New wine in old bottles: current progress on P5 ATPases

P5 ATPases are evolutionarily conserved P-type transporters. Despite their important roles in the endoplasmic reticulum (ER) and in lysosomes, the substrate specificities and transporting mechanisms of P5 ATPases have remained mysterious. Recently, several studies have provided genetic, biochemical, and structural evidence to help elucidate the physiological functions and substrates of P5 ATPases. Here, we summarize this progress and discuss the potential transport mechanisms of the P5 ATPases-in particular, P5A ATPase-for further study.

The Endoplasmic Reticulum ATP13A1 is Essential for MAVS-Mediated Antiviral Innate Immunity

RIG-I-MAVS signaling pathway is essential for efficient innate immune response against virus infection. Though many components have been identified in RIG-I pathway and it can be partially reconstituted in vitro, detailed mechanisms involved in cells are still unclear. Here, a genome-wide CRISPR-Cas9 screen is performed using an engineered cell line IFNB-P2A-GSDMD-N, and ATP13A1, a putative dislocase located on the endoplasmic reticulum, is identified as an important regulator of RIG-I pathway. ATP13A1 deficiency abolishes RIG-I-mediated antiviral innate immune response due to compromised MAVS stability and crippled signaling potency of residual MAVS. Moreover, it is discovered that MAVS is subject to protease-mediated degradation in the absence of ATP13A1. As homozygous Atp13a1 knockout mice result in developmental retardation and embryonic lethality, Atp13a1 conditional knockout mice are generated. Myeloid-specific Atp13a1-deficient mice are viable and susceptible to RNA virus infection. Collectively, the findings reveal that ATP13A1 is indispensable for the stability and activation of MAVS and a proper antiviral innate immune response.

The Function, Structure, and Origins of the ER Membrane Protein Complex

The endoplasmic reticulum (ER) is the site of membrane protein insertion, folding, and assembly in eukaryotes. Over the past few years, a combination of genetic and biochemical studies have implicated an abundant factor termed the ER membrane protein complex (EMC) in several aspects of membrane protein biogenesis. This large nine-protein complex is built around a deeply conserved core formed by the EMC3-EMC6 subcomplex. EMC3 belongs to the universally conserved Oxa1 superfamily of membrane protein transporters, whereas EMC6 is an ancient, widely conserved obligate partner. EMC has an established role in the insertion of transmembrane domains (TMDs) and less understood roles during the later steps of membrane protein folding and assembly. Several recent structures suggest hypotheses about the mechanism(s) of TMD insertion by EMC, with various biochemical and proteomics studies beginning to reveal the range of EMC's membrane protein substrates. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The endoplasmic reticulum P5A-ATPase is a transmembrane helix dislocase

Organelle identity depends on protein composition. How mistargeted proteins are selectively recognized and removed from organelles is incompletely understood. Here, we found that the orphan P5A-adenosine triphosphatase (ATPase) transporter ATP13A1 (Spf1 in yeast) directly interacted with the transmembrane segment (TM) of mitochondrial tail-anchored proteins. P5A-ATPase activity mediated the extraction of mistargeted proteins from the endoplasmic reticulum (ER). Cryo-electron microscopy structures of Saccharomyces cerevisiae Spf1 revealed a large, membrane-accessible substrate-binding pocket that alternately faced the ER lumen and cytosol and an endogenous substrate resembling an α-helical TM. Our results indicate that the P5A-ATPase could dislocate misinserted hydrophobic helices flanked by short basic segments from the ER. TM dislocation by the P5A-ATPase establishes an additional class of P-type ATPase substrates and may correct mistakes in protein targeting or topogenesis.

Parkinson disease related ATP13A2 evolved early in animal evolution

Several human P5-type transport ATPases are implicated in neurological disorders, but little is known about their physiological function and properties. Here, we investigated the relationship between the five mammalian P5 isoforms ATP13A1-5 in a comparative study. We demonstrated that ATP13A1-4 isoforms undergo autophosphorylation, which is a hallmark P-type ATPase property that is required for substrate transport. A phylogenetic analysis of P5 sequences revealed that ATP13A1 represents clade P5A, which is highly conserved between fungi and animals with one member in each investigated species. The ATP13A2-5 isoforms belong to clade P5B and diversified from one isoform in fungi and primitive animals to a maximum of four in mammals by successive gene duplication events in vertebrate evolution. We revealed that ATP13A1 localizes in the endoplasmic reticulum (ER) and experimentally demonstrate that ATP13A1 likely contains 12 transmembrane helices. Conversely, ATP13A2-5 isoforms reside in overlapping compartments of the endosomal system and likely contain 10 transmembrane helices, similar to what was demonstrated earlier for ATP13A2. ATP13A1 complemented a deletion of the yeast P5A ATPase SPF1, while none of ATP13A2-5 could complement either the loss of SPF1 or that of the single P5B ATPase YPK9 in yeast. Thus, ATP13A1 carries out a basic ER function similar to its yeast counterpart Spf1p that plays a role in ER related processes like protein folding and processing. ATP13A2-5 isoforms diversified in mammals and are expressed in the endosomal system where they may have evolved novel complementary or partially redundant functions. While most P5-type ATPases are widely expressed, some P5B-type ATPases (ATP13A4 and ATP13A5) display a more limited tissue distribution in the brain and epithelial glandular cells, where they may exert specialized functions. At least some P5B isoforms are of vital importance for the nervous system, since ATP13A2 and ATP13A4 are linked to respectively Parkinson disease and autism spectrum disorders.

Differential Roles for Six P-Type Calcium ATPases in Sustaining Intracellular Ca2+ Homeostasis, Asexual Cycle and Environmental Fitness of Beauveria bassiana

A global insight into the roles of multiple P-type calcium ATPase (CA) pumps in sustaining the life of a filamentous fungal pathogen is lacking. Here we elucidated the functions of five CA pumps (Eca1, Spf1 and PmcA/B/C) following previous characterization of Pmr1 in Beauveria bassiana, a fungal insect pathogen. The fungal CA pumps interacted at transcriptional level, at which singular deletions of five CA genes depressed eca1 expression by 76–98% and deletion of spf1 resulted in drastic upregulation of four CA genes by 36–50-fold. Intracellular Ca²⁺ concentration increased differentially in most deletion mutants exposed to the stresses of Ca²⁺, EDTA chelator, and/or endoplasmic reticulum and calcineurin inhibitors, accompanied with their changed sensitivities to not only the mentioned agents but also Fe²⁺, Cu²⁺ and Zn²⁺. Liquid culture acidification was delayed in the Δspf1, Δpmr1 and ΔpmcA mutants, coinciding well with altered levels of their extracellular lactic and oxalic acids. Moreover, all deletion mutants showed differential defects in conidial germination, vegetative growth, conidiation capacity, antioxidant activity, cell wall integrity, conidial UV-B resistance and/or virulence. Our results provide the first global insight into differential roles for six CA pumps in sustaining intracellular Ca²⁺ level, asexual cycle and environmental fitness of B. bassiana.

Congenital heart disease protein 5 associates with CASZ1 to maintain myocardial tissue integrity

The identification and characterization of the cellular and molecular pathways involved in the differentiation and morphogenesis of specific cell types of the developing heart are crucial to understanding the process of cardiac development and the pathology associated with human congenital heart disease. Here, we show that the cardiac transcription factor CASTOR (CASZ1) directly interacts with congenital heart disease 5 protein (CHD5), which is also known as tryptophan-rich basic protein (WRB), a gene located on chromosome 21 in the proposed region responsible for congenital heart disease in individuals with Down's syndrome. We demonstrate that loss of CHD5 in Xenopus leads to compromised myocardial integrity, improper deposition of basement membrane, and a resultant failure of hearts to undergo cell movements associated with cardiac formation. We further report that CHD5 is essential for CASZ1 function and that the CHD5-CASZ1 interaction is necessary for cardiac morphogenesis. Collectively, these results establish a role for CHD5 and CASZ1 in the early stages of vertebrate cardiac development.

Towards defining the substrate of orphan P5A-ATPases

BACKGROUND

P-type ATPases are ubiquitous ion and lipid pumps found in cellular membranes. P5A-ATPases constitute a poorly characterized subfamily of P-type ATPases present in all eukaryotic organisms but for which a transported substrate remains to be identified.

SCOPE OF REVIEW

This review aims to discuss the available evidence which could lead to identification of possible substrates of P5A-ATPases.

MAJOR CONCLUSIONS

The complex phenotypes resulting from the loss of P5A-ATPases in model organisms can be explained by a role of the P5A-ATPase in the endoplasmic reticulum (ER), where loss of function leads to broad and unspecific phenotypes related to the impairment of basic ER functions such as protein folding and processing. Genetic interactions in Saccharomyces cerevisiae point to a role of the endogenous P5A-ATPase Spf1p in separation of charges in the ER, in sterol metabolism, and in insertion of tail-anchored proteins in the ER membrane. A role for P5A-ATPases in vesicle formation would explain why sterol transport and distribution are affected in knock out cells, which in turn has a negative impact on the spontaneous insertion of tail-anchored proteins. It would also explain why secretory proteins destined for the Golgi and the cell wall have difficulties in reaching their final destination. Cations and phospholipids could both be transported substrates of P5A-ATPases and as each carry charges, transport of either might explain why a charge difference arises across the ER membrane.

GENERAL SIGNIFICANCE

Identification of the substrate of P5A-ATPases would throw light on an important general process in the ER that is still not fully understood. This article is part of a Special Issue entitled Structural biochemistry and biophysics of membrane proteins.

Ergosterol content specifies targeting of tail-anchored proteins to mitochondrial outer membranes

Mitochondrial outer membrane tail-anchored proteins are a unique class of membrane proteins with unknown targeting mechanism. Using two high-throughput microscopy screens, we demonstrate that the inherent differences in membrane composition between organelle membranes is enough to determine membrane integration specificity in a living cell.

Tail-anchored (TA) proteins have a single C-terminal transmembrane domain, making their biogenesis dependent on posttranslational translocation. Despite their importance, no dedicated insertion machinery has been uncovered for mitochondrial outer membrane (MOM) TA proteins. To decipher the molecular mechanisms guiding MOM TA protein insertion, we performed two independent systematic microscopic screens in which we visualized the localization of model MOM TA proteins on the background of mutants in all yeast genes. We could find no mutant in which insertion was completely blocked. However, both screens demonstrated that MOM TA proteins were partially localized to the endoplasmic reticulum (ER) in ∆spf1 cells. Spf1, an ER ATPase with unknown function, is the first protein shown to affect MOM TA protein insertion. We found that ER membranes in ∆spf1 cells become similar in their ergosterol content to mitochondrial membranes. Indeed, when we visualized MOM TA protein distribution in yeast strains with reduced ergosterol content, they phenocopied the loss of Spf1. We therefore suggest that the inherent differences in membrane composition between organelle membranes are sufficient to determine membrane integration specificity in a eukaryotic cell.

Decreased expression of chromodomain helicase DNA-binding protein 5 is an unfavorable prognostic marker in patients with primary gallbladder carcinoma

AIM

Chromodomain helicase DNA-binding protein 5 (CHD5) plays a role in normal neural development and in tumorigenesis of various human cancers. However, its role in primary gallbladder carcinoma (PGC) is still unclear. The aim of this study was to investigate CHD5 expression in PGC and its clinical significance.

METHODS

CHD5 mRNA and protein expression in 120 PGC and 20 normal gallbladder specimens was determined by quantitative reverse transcription-polymerase chain reaction (QRT-PCR) and Western blotting analysis, respectively.

RESULTS

The expression levels of CHD5 mRNA and protein in PGC tissues were both significantly lower than those in the normal epithelium of the gallbladder (mRNA: P = 0.006; protein: P = 0.01). CHD5 mRNA expression was closely correlated with its protein expression (r = 0.8; P < 0.001). Additionally, the low expression of CHD5 protein was significantly associated with high pathologic T stage (P = 0.01) and clinical stage (P = 0.008), and advanced histologic grade (P = 0.009). The expression levels of CHD5 protein in PGC tissues with positive nodal metastasis were also significantly lower than those without (P = 0.01). Survival analysis showed that low CHD5 expression was associated with shorter disease-free (P = 0.01) and overall survival (P = 0.008) compared to those with high CHD5 expression in PGC patients. Furthermore, multivariate analyses showed that the decreased expression of CHD5 was an independent prognostic marker for both unfavorable disease-free (P = 0.01) and overall survival (P = 0.006).

CONCLUSION

CHD5 may be involved in carcinogenesis of PGC and its down-regulation may be significantly correlated with unfavorable clinicopathologic features including poor overall and disease-free survival in patients.

Ca2+ induces spontaneous dephosphorylation of a novel P5A-type ATPase

P5 ATPases constitute the least studied group of P-type ATPases, an essential family of ion pumps in all kingdoms of life. Although P5 ATPases are present in every eukaryotic genome analyzed so far, they have remained orphan pumps, and their biochemical function is obscure. We show that a P5A ATPase from barley, HvP5A1, locates to the endoplasmic reticulum and is able to rescue knock-out mutants of P5A genes in both Arabidopsis thaliana and Saccharomyces cerevisiae. HvP5A1 spontaneously forms a phosphorylated reaction cycle intermediate at the catalytic residue Asp-488, whereas, among all plant nutrients tested, only Ca(2+) triggers dephosphorylation. Remarkably, Ca(2+)-induced dephosphorylation occurs at high apparent [Ca(2+)] (K(i) = 0.25 mM) and is independent of the phosphatase motif of the pump and the putative binding site for transported ligands located in M4. Taken together, our results rule out that Ca(2+) is a transported substrate but indicate the presence of a cytosolic low affinity Ca(2+)-binding site, which is conserved among P-type pumps and could be involved in pump regulation. Our work constitutes the first characterization of a P5 ATPase phosphoenzyme and points to Ca(2+) as a modifier of its function.

Whole blood genomic biomarkers of acute cardiac allograft rejection

BACKGROUND

Significant progress has been made in cardiac transplantation over the past 30 years; however, the means for detection of acute cardiac allograft rejection remains in need of improvement. At present, the endomyocardial biopsy, an invasive and inconvenient procedure for patients, is required for the surveillance and diagnosis of acute cardiac allograft rejection. In the Biomarkers in Transplantation initiative, we investigated gene expression profiles in peripheral blood of cardiac transplant subjects as potential biomarkers for diagnosis of allograft rejection.

METHODS

Whole blood samples were obtained from 28 cardiac transplant subjects who consented to the study. Serial samples were collected from pre-transplant through 3 years post-transplant according to the standard protocol. Temporally correspondent biopsies were also collected, reviewed in a blinded manner, and graded according to current ISHLT guidelines. Blood samples were analyzed using Affymetrix microarrays. Genomic profiles were compared in subjects with acute rejection (AR; ISHLT Grade > or =2R) and no rejection (NR; Grade 0R). Biomarker panel genes were identified using linear discriminant analysis.

RESULTS

We found 1,295 differentially expressed probe-sets between AR and NR samples and developed a 12-gene biomarker panel that classifies our internal validation samples with 83% sensitivity and 100% specificity.

CONCLUSIONS

Based on our current results, we believe whole blood genomic biomarkers hold great potential in the diagnosis of acute cardiac allograft rejection. A prospective, Canada-wide trial will be conducted shortly to further evaluate the classifier panel in diverse patients and a range of clinical programs.

Local coherence in genetic interaction patterns reveals prevalent functional versatility

MOTIVATION

Epistatic or genetic interactions, representing the effects of mutating one gene on the phenotypes caused by mutations in one or more distinct genes, can be very helpful for uncovering functional relationships between genes. Recently, the epistatic miniarray profiles (E-MAP) method has emerged as a powerful approach for identifying such interactions systematically. For E-MAP data analysis, hierarchical clustering is used to partition genes into groups on the basis of the similarity between their global interaction profiles, and the resulting descriptions assign each gene to only one group, thereby ignoring the multifunctional roles played by most genes.

RESULTS

Here, we present the original local coherence detection (LCD) algorithm for identifying groups of functionally related genes from E-MAP data in a manner that allows individual genes to be assigned to more than one functional group. This enables investigation of the pleiotropic nature of gene function. The performance of our algorithm is illustrated by applying it to two E-MAP datasets and an E-MAP-like in silico dataset for the yeast Saccharomyces cerevisiae. In addition to recapitulating the majority of the functional modules and many protein complexes reported previously, our algorithm uncovers many recently documented and novel multifunctional relationships between genes and gene groups. Our algorithm hence represents a valuable tool for uncovering new roles for genes with annotated functions and for mapping groups of genes and proteins into pathways.

EOS1, whose deletion confers sensitivity to oxidative stress, is involved in N-glycosylation in Saccharomyces cerevisiae

The deletion strain of Saccharomyces cerevisiae YNL080c (designed as EOS1) was identified as a strain sensitive to high-sucrose stress in our previous report [A. Ando, F. Tanaka, Y. Murata, H. Takagi, J. Shima, Identification and classification of genes required for tolerance to high sucrose stress revealed by genome-wide screening of Saccharomyces cerevisiae, FEMS Yeast Res. 6 (2006) 249-267]. Delta eos1 showed higher sensitivity to oxidative stress than to high-sucrose stress. Immunofluorescence microscopic and cellular fractionation analyses suggested that Eos1 localizes in the endoplasmic reticulum membrane. We found that the deletion of EOS1 enhances tunicamycin tolerance and that in Delta eos1 the transcription level of KAR2, which is the ER stress-inducible gene, was much lower than that in the wild-type strain (BY4741) when exposed to tunicamycin. The inhibition of the N-glycosylation of carboxypeptidase Y and invertase activity caused by the addition of tunicamycin was depressed in Delta eos1, suggesting that EOS1 may be involved in N-glycosylation of the cellular proteins.