Nonsense-mediated mRNA decay of mRNAs encoding a signal peptide occurs primarily after mRNA targeting to the endoplasmic reticulum

Translation of messenger ribonucleic acids (mRNAs) encoding integral membrane proteins or secreted proteins occurs on the surface of the endoplasmic reticulum (ER). When a nascent signal peptide is synthesized from the mRNAs, the ribosome-nascent chain complex (RNC) is recognized by the signal recognition particle (SRP) and then transported to the surface of the ER. The appropriate targeting of the RNC-SRP complex to the ER is monitored by a quality control pathway, a nuclear cap-binding complex (CBC)-ensured translational repression of RNC-SRP (CENTRE). In this study, using ribosome profiling of CBC-associated and eukaryotic translation initiation factor 4E-associated mRNAs, we reveal that, at the transcriptomic level, CENTRE is in charge of the translational repression of the CBC-RNC-SRP until the complex is specifically transported to the ER. We also find that CENTRE inhibits the nonsense-mediated mRNA decay (NMD) of mRNAs within the CBC-RNC-SRP. The NMD occurs only after the CBC-RNC-SRP is targeted to the ER and after eukaryotic translation initiation factor 4E replaces CBC. Our data indicate dual surveillance for properly targeting mRNAs encoding integral membrane or secretory proteins to the ER. CENTRE blocks gene expression at the translation level before the CBC-RNC-SRP delivery to the ER, and NMD monitors mRNA quality after its delivery to the ER.

Protein biomarkers for root length and root dry mass on chromosomes 4A and 7A in wheat

Improving the wheat (Triticum aestivum L.) root system is important for enhancing grain yield and climate resilience. Total root length (RL) and root dry mass (RM) significantly contribute to water and nutrient acquisition directly impacting grain yield and stress tolerance. This study used label-free quantitative proteomics to identify proteins associated with RL and RM in wheat near-isogenic lines (NILs). NIL pair 6 had 113 and NIL pair 9 had 30 differentially abundant proteins (DAPs). Three of identified DAPs located within the targeted genomic regions (GRs) of NIL pairs 6 (qDT.4A.1) and 9 (QHtscc.ksu-7A), showed consistent gene expressions at the protein and mRNA transcription (qRT-PCR) levels for asparagine synthetase (TraesCS4A02G109900), signal recognition particle 19 kDa protein (TraesCS7A02G333600) and 3,4-dihydroxy-2-butanone 4-phosphate synthase (TraesCS7A02G415600). This study discovered, for the first time, the involvement of these proteins as candidate biomarkers for increased RL and RM in wheat. However, further functional validation is required to ascertain their practical applicability in wheat root breeding. SIGNIFICANCE OF THE STUDY: Climate change has impacted global demand for wheat (Triticum aestivum L.). Root traits such as total root length (RL) and root dry mass (RM) are crucial for water and nutrient uptake and tolerance to abiotic stresses such as drought, salinity, and nutrient imbalance in wheat. Improving RL and RM could significantly enhance wheat grain yield and climate resilience. However, breeding for these traits has been limited by lack of appropriate root phenotyping methods, advanced genotypes, and the complex nature of the wheat genome. In this study, we used a semi-hydroponic root phenotyping system to collect accurate root data, near-isogenic lines (NILs; isolines with similar genetic backgrounds but contrasting target genomic regions (GRs)) and label-free quantitative proteomics to explore the molecular mechanisms underlying high RL and RM in wheat. We identified differentially abundant proteins (DAPs) and their molecular pathways in NIL pairs 6 (GR: qDT.4A.1) and 9 (GR: QHtscc.ksu-7A), providing a foundation for further molecular investigations. Furthermore, we identified three DAPs within the target GRs of the NIL pairs with differential expression at the transcript level, as confirmed by qRT-PCR analysis which could serve as candidate protein biomarkers for RL and RM improvement.

Therapeutic management of immune-mediated necrotizing myositis

Purpose of Review

The idiopathic inflammatory myopathies are a heterogeneous group of autoimmune disorders characterized by skeletal muscle inflammation leading to chronic muscle weakness. Immune-mediated necrotizing myopathy (IMNM) is a distinct subgroup of inflammatory myopathy typically characterized by myofiber necrosis with minimal inflammatory infiltrates on muscle biopsy, highly elevated creatine kinase levels, and infrequent extra-muscular involvement. This review provides an overview of currently recommended treatment strategies for IMNM, including discussion of disease activity monitoring and recommended first-line immunomodulatory agents depending on clinical phenotype and autoantibody status.

Recent Findings

IMNM can be divided into three subtypes based on autoantibody positivity: anti-3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR) IMNM, anti-signal recognition particle (SRP) IMNM, and antibody negative IMNM. Autoantibody status in IMNM has considerable correlation with clinical phenotype, prognosis, and recommended choice of immunosuppressive agent. Patients with anti-HMGCR IMNM tend to respond well to intravenous immunoglobulin (IVIG), and IVIG monotherapy may be sufficient treatment for certain patients. In anti-SRP IMNM, early rituximab is commonly favored. More generally, prompt initiation of aggressive immunosuppression is often indicated, as both anti-SRP and anti-HMGCR IMNM can potentially cause debilitating weakness, and muscle atrophy and irreversible fatty replacement happen early in the disease course. Patients with IMNM frequently require combination therapy to achieve disease control, and have a high rate of relapse when tapering immunosuppression. Young age of onset is a poor prognostic factor.

Summary

IMNM can be severely disabling and often requires aggressive immunosuppression. For any given patient, the treatment strategy should be informed by the severity of their presenting features and autoantibody status. While our ability to treat IMNM has certainly improved, there remains a need for more prospective trials to inform optimal treatment strategies.

Archaeal SRP RNA and SRP19 facilitate the assembly of SRP54-FtsY targeting complex

The signal recognition particle (SRP) plays an essential role in protein translocation across biological membranes. Stable complexation of two GTPases in the signal recognition particle (SRP) and its receptor (SR) control the delivery of nascent polypeptide to the membrane translocon. In archaea, protein targeting is mediated by the SRP54/SRP19/7S RNA ribonucleoprotein complex (SRP) and the FtsY protein (SR). In the present study, using fluorescence resonance energy transfer (FRET), we demonstrate that archaeal 7S RNA stabilizes the SRP54·FtsY targeting complex (TC). Moreover, we show that archaeal SRP19 further assists 7S RNA in stabilizing the targeting complex (TC). These results suggest that archaeal 7S RNA and SRP19 modulate the conformation of the targeting complex and thereby reinforce TC to execute protein translocation via concomitant GTP hydrolysis.

Myopathy associated with anti-signal recognition particle antibodies with pulmonary involvement and response to rituximab

The authors present the case of a 76-year-old female patient with progressive decrease in proximal muscle strength, fatigue, dyspnea, diffuse hand edema and painful triphasic Raynaud's phenomenon. Anti-SRP and anti-SSA antibodies were detected, muscle biopsy revealed changes consistent with necrotizing myopathy and capillaroscopy had findings compatible with systemic sclerosis. High-resolution chest computed tomography revealed interstitial lung disease with a non-specific interstitial pneumonia pattern. Lung function tests demonstrated a forced vital capacity 93% and a diffusing capacity for carbon monoxide of 65% predicted. After multidisciplinary discussion, she was diagnosed with immune-mediated necrotizing myopathy/systemic sclerosis overlap syndrome with pulmonary involvement. Initially, dual immunomodulation therapy with high-dose steroids and intravenous immunoglobulin was started, but after 4 weeks, the patient had clinical and analytical deterioration. At this time, she was started on rituximab, with an excellent and sustained response at both muscle and lung, sustained after 12 months.

Chloroplast SRP54s are Essential for Chloroplast Development in Rice

BACKGROUND

The chloroplast signal recognition particle 54 (cpSRP54) is known for targeting the light-harvesting complex proteins to thylakoids and plays a critical role for chloroplast development in Arabidopsis, but little is known in rice. Here, we reported two homologous cpSRP54s that affect chloroplast development and plant survival in rice.

RESULTS

Two rice cpSRP54 homologues, OscpSRP54a and OscpSRP54b, were identified in present study. The defective OscpSRP54a (LOC_Os11g05552) was responsible for the pale green leaf phenotype of the viable pale green leaf 14 (pgl14) mutant. A single nucleotide substitution from G to A at the position 278, the first intron splicing site, was detected in LOC_Os11g05552 in pgl14. The wild type allele could rescue the mutant phenotype. Knockout lines of OscpSRP54b (LOC_Os11g05556) exhibited similar pale green phenotype to pgl14 with reduced chlorophyll contents and impaired chloroplast development, but showed apparently arrested-growth and died within 3 weeks. Both OscpSRP54a and OscpSRP54b were constitutively expressed mainly in shoots and leaves at the vegetative growth stage. Subcellular location indicated that both OscpSRP54a and OscpSRP54b were chloroplast-localized. Both OscpSRP54a and OscpSRP54b were able to interact with OscpSRP43, respectively. The transcript level of OscpSRP43 was significantly reduced while the transcript level of OscpSRP54b was apparently increased in pgl14. In contrast, the transcript levels of OscpSRP54a, OscpSRP43 and OscpSRP54b were all significantly decreased in OscpSRP54b knockout lines.

CONCLUSION

Our study demonstrated that both OscpSRP54a and OscpSRP54b were essential for normal chloroplast development by interacting with OscpSRP43 in rice. OscpSRP54a and OscpSRP54b might play distinct roles in transporting different chloroplast proteins into thylakoids through cpSRP-mediated pathway.

Structural insights into the G-loop dynamics of E. coli FtsY NG domain

The bacterial signal recognition particle (SRP) receptor, FtsY, participates with the SRP in co-translation targeting of proteins. Multiple crystal structures of the NG domain of E. coli FtsY_NG have been determined at high-resolution (1.22-1.88 Å), in the nucleotide-free (apo) form as well as bound to GDP and non-hydrolysable GTP analogues. The combination of high-resolution and multiple solved structures of FtsY_NG in different states revealed a new sensor-relay system of this unique GTPase receptor. A nucleotide sensing function of the P-loop assists FtsY_NG in nucleotide-binding and contributes to modulate nucleotide binding properties in SRP GTPases. A reorganization of the other G-loops and the insertion binding domain (IBD) is observed only upon transition from a diphosphate to a triphosphate nucleotide. The role of a magnesium ion during the GDP and GTP-bound states has also been observed. The binding of magnesium in the nucleotide site causes the reorientation of the β- and γ- phosphate groups toward the jaws of the P-loop and stabilizes the binding of the nucleotide, creating a network of hydrogen and water-bridge interactions.

In vivo assembly of eukaryotic signal recognition particle: A still enigmatic process involving the SMN complex

The signal recognition particle (SRP) is a universally conserved non-coding ribonucleoprotein complex that is essential for targeting transmembrane and secretory proteins to the endoplasmic reticulum. Its composition and size varied during evolution. In mammals, SRP contains one RNA molecule, 7SL RNA, and six proteins: SRP9, 14, 19, 54, 68 and 72. Despite a very good understanding of the SRP structure and of the SRP assembly in vitro, how SRP is assembled in vivo remains largely enigmatic. Here we review current knowledge on how the 7SL RNA is assembled with core proteins to form functional RNP particles in cells. SRP biogenesis is believed to take place both in the nucleolus and in the cytoplasm and to rely on the survival of motor neuron complex, whose defect leads to spinal muscular atrophy.

Hydrophobicity, rather than secondary structure, is essential for the SRP dependent targeting of GPR35 to the ER membrane

The folding and targeting of hydrophobic transmembrane domains poses a major challenge to the cell. Several membrane proteins have been shown to gain some degree of secondary structure within the ribosome tunnel and to retain this conformation throughout maturation. However, there is little information on one of the largest classes of eukaryotic membrane proteins; the G protein-coupled receptors (GPCRs). In this study we show that the signal anchor domain of GPR35 remains in an extended conformation whilst exiting the ribosome tunnel, the polypeptide chain then forms interactions with components of the SRP targeting pathway, and the Sec61 translocon, resulting in a compacted conformation prior to integration into the ER membrane. We conclude that transmembrane structure is most likely adopted after the domain leaves the ribosome tunnel and that the interaction of the signal anchor with SRP is dependent on the native levels of hydrophobicity within the first transmembrane domain. Therefore, we propose a mechanism by which the first transmembrane domains of multi-spanning membrane proteins adopt compacted structures following SRP targeting but before insertion into the ER membrane.

Myositis-specific autoantibodies, a cornerstone in immune-mediated necrotizing myopathy

Over the past few years, myositis-specific autoantibodies played an increasing role in the inflammatory idiopathic myositis definition. They became the critical immunological marker for immune-mediated necrotizing myopathy diagnosis (IMNM) since the paradigm switch from histological to serological criteria. This review is focused on the key role of the anti-signal recognition particle (anti-SRP) and the anti-3-Hydroxy-3-MethylGlutaryl-Coenzyme A Reductase (anti-HMGCR) antibodies in immune-mediated necrotizing myopathy. Anti-SRP and anti-HMGCR antibodies are robust diagnostic tools in case of both the classical subacute form and the slowly progressive form of IMNM that may mimic muscular dystrophy. Anti-SRP and anti-HMGCR patients share clinical, biological and histological features with some antibody-associated specificity. Anti-SRP patients harbour more severe muscle weakness and atrophy with severe muscle damage on magnetic resonance imaging study. Approximately 10-20% of anti-SRP patients develop extramuscular symptoms, especially lung interstitial disease. Conversely, anti-HMGCR patients are often associated with statin exposure. In both cases, patients have a poor outcome with frequent relapse and the use of combined immunotherapy. Of note, various data suggest a direct pathogenic role of these antibodies reinforcing the interest in targeted therapeutic strategy.

Immune-Mediated Necrotizing Myopathy

PURPOSE OF REVIEW

Immune-mediated necrotizing myopathy (IMNM) is a type of autoimmune myopathy characterized by relatively severe proximal weakness, myofiber necrosis with minimal inflammatory cell infiltrate on muscle biopsy, and infrequent extra-muscular involvement. Here, we will review the characteristics of patients with IMNM.

RECENT FINDINGS

Anti-signal recognition particle (SRP) and anti-hydroxy-3-methylglutaryl-CoA reductase (HMGCR) autoantibodies are closely associated with IMNM and define unique subtypes of patients. Importantly, the new European Neuromuscular Centre criteria recognize anti-SRP myopathy, anti-HMGCR myopathy, and autoantibody-negative IMNM as three distinct subtypes of IMNM. Anti-SRP myopathy patients have more severe muscle involvement, have more common extra-muscular features, and may respond best to immunosuppressive regimens that include rituximab. In contrast, anti-HMGCR myopathy is often associated with statin exposure and intravenous immunoglobulin treatment may be an effective treatment, even as monotherapy. Both anti-SRP and anti-HMGCR myopathy tend to be most severe in younger patients. Furthermore, children with these forms of IMNM may present with dystrophy-like features which are potentially reversible with immunosuppressant treatment. IMNM patients with either autoantibody may experience fatty replacement of muscle soon after disease onset, suggesting that intense and early immunosuppressant therapy may provide the best chance to avoid long-term disability. IMNM is composed of anti-SRP myopathy, anti-HMGCR myopathy, and autoantibody-negative IMNM. Both anti-SRP and anti-HMGCR myopathy can cause severe weakness, especially in younger patients. Anti-SRP myopathy patients tend to have the most severe weakness and most prevalent extra-muscular features. Autoantibody-negative IMNM remains poorly described.

Diverse role of survival motor neuron protein

The multifunctional Survival Motor Neuron (SMN) protein is required for the survival of all organisms of the animal kingdom. SMN impacts various aspects of RNA metabolism through the formation and/or interaction with ribonucleoprotein (RNP) complexes. SMN regulates biogenesis of small nuclear RNPs, small nucleolar RNPs, small Cajal body-associated RNPs, signal recognition particles and telomerase. SMN also plays an important role in DNA repair, transcription, pre-mRNA splicing, histone mRNA processing, translation, selenoprotein synthesis, macromolecular trafficking, stress granule formation, cell signaling and cytoskeleton maintenance. The tissue-specific requirement of SMN is dictated by the variety and the abundance of its interacting partners. Reduced expression of SMN causes spinal muscular atrophy (SMA), a leading genetic cause of infant mortality. SMA displays a broad spectrum ranging from embryonic lethality to an adult onset. Aberrant expression and/or localization of SMN has also been associated with male infertility, inclusion body myositis, amyotrophic lateral sclerosis and osteoarthritis. This review provides a summary of various SMN functions with implications to a better understanding of SMA and other pathological conditions.

Immune-mediated necrotizing myopathy, associated with antibodies to signal recognition particle, together with lupus nephritis: case presentation and management

A male patient with limb weakness, myalgia and edema was subsequently found to have an immune-mediated necrotizing myopathy (IMNM) on biopsy. Targeted myopathic antibody analysis revealed antibodies to signal recognition particle (SRP). Anti-SRP-associated necrotizing myopathy was diagnosed. This case was complicated by the concurrent development of class III lupus nephritis. We discuss an interesting case progression and development as well as the management of these difficult to treat conditions.

Novel antibody associations in immune-mediated necrotising myopathy without inflammation

INTRODUCTION

The patient presenting with proximal muscle weakness, elevated serum creatinine kinase and myopathic electromyography and biopsy findings has a wide differential diagnosis that includes toxic, autoimmune, paraneoplastic and congenital myopathies. Autoimmune myopathies are important to identify because they may respond to immunosuppressive therapies.

METHODS

We describe two cases of immune-mediated necrotizing myopathy each associated with a novel antibody.

RESULTS

Case 1 describes a progressive myopathy in a statin user. Antibodies to 3-hydroxy-3-methyl-glutaryl-coenzyme A reductase were identified and the patient responded to steroid therapy. Case 2 describes an aggressive myopathy associated with antibodies to signal recognition particle. There was no response to steroids. Clinical improvement followed treatment with rituximab and cyclophosphamide.

CONCLUSION

The identification of myositis-specific antibodies is important because they are associated with distinct clinical phenotypes and may guide the physician in terms of treatment strategies.

Clinical and histological findings associated with autoantibodies detected by RNA immunoprecipitation in inflammatory myopathies

Of 207 adult patients with idiopathic inflammatory myopathies, detection of autoantibodies by RNA immunoprecipitation showed that 99 patients (48%) were antibody-positive. We divided these 99 into five subgroups: anti-signal recognition particle (SRP), anti-aminoacyl transfer RNA synthetase, anti-Ku, anti-U1RNP, and anti-SSA/B. Younger age at onset, severe weakness, muscle atrophy, elevated creatine kinase, and necrosis in muscle fibers without inflammatory cell infiltration were found significantly more frequently among the patients with anti-SRP antibodies (n=41) compared to the antibody-negative patients (n=108). Autoantibody detection by RNA immunoprecipitation can provide useful information associated with clinical and histological findings.

[Usefulness of autoantibodies for the diagnosis of autoimmune myopathies]

INTRODUCTION

Idiopathic myopathies are a group of acquired muscular diseases considered as autoimmune disorders. Characteristic histopathologic features allow the classification into myositis (polymyositis, dermatomyositis, and inclusion body myositis) and immune-mediated necrotizing myopathies. But overlapping histological features may be observed between different idiopathic myopathies and even between acquired and genetic muscular diseases. In the group of idiopathic myopathies important discrepancies can be observed concerning extra-muscular involvement and prognosis.

STATE OF ART

The discovery of myositis-specific antibodies and myositis-associated antibodies has led to a serologic approach complementary to histological classification, because striking associations of myositis-specific antibodies with clinical features and survival were observed. Here we reviewed the myositis-specific antibodies including autoantibodies directed against the aminoacyl tRNA-synthetase enzymes, the Mi-2 protein and the signal recognition particle, and the main myositis-associated autoantibodies, that can be tested in clinical practice.

PERSPECTIVES

We will also focus on newly described dermatomyositis-associated antibodies (directed against: transcription intermediary factor 1 family proteins, small ubiquitin-like modifier activating enzyme, and melanoma differentiation-associated gene 5), and immune-mediated necrotizing myopathy-associated antibodies (directed against HMGcoA-reductase).

CONCLUSION

Myositis-specific antibodies and myositis-associated antibodies are useful for the diagnosis of forms of autoimmune myopathies with distinct clinical features. They may help to define patients into clinical syndromes with specific outcomes and thus influence treatment strategies.

Take the (RN)A-train: localization of mRNA to the endoplasmic reticulum

Protein translocation into the endoplasmic reticulum (ER) generally requires targeting of mRNAs encoding secreted or membrane proteins to the ER membrane. The prevalent view is that these mRNAs are delivered co-translationally, using the signal recognition particle (SRP) pathway. Here, SRP delivers signal sequence-containing proteins together with associated ribosomes and mRNA to the SRP receptor present on the ER surface. Recent studies demonstrate the presence of alternative pathways to recruit mRNAs to ER or to specific subdomains of the ER independent of SRP or translation. Such targeting of specific mRNAs to the ER subdomains allows the cell to sort proteins before translocation or to ensure co-localization of ER and mRNAs at specific locations. Translation-independent association of mRNAs involves ER-linked RNA-binding proteins and represents an alternative pathway of mRNA delivery to the ER. This article is part of a Special Issue entitled: Functional and structural diversity of endoplasmic reticulum.