Two-step membrane binding by the bacterial SRP receptor enable efficient and accurate Co-translational protein targeting

Unravelling the role of the A domain and N-terminal alpha-helices of FtsY in archaeal signal recognition particle

Signal recognition particle (SRP) system is critical for protein translocation across membranes in all domains of life. In archaea, this pathway relies on two GTPase proteins, SRP54 and FtsY, which interact with SRP RNA to facilitate the targeting of nascent proteins to the membrane. Although the SRP components in eukaryotes and bacteria are well characterized, the mechanisms underlying SRP-dependent membrane targeting in archaea remain poorly understood, particularly concerning the role of the FtsY N-terminal domains. This study provides an in-depth exploration of the archaeal SRP system, focusing on the N-terminal domains of the FtsY protein and their role in the formation and functionality of the targeting complex (TC). We characterized the minimal structural domains of FtsY required for SRP54 binding and membrane association, demonstrating the critical involvement of the A domain and N-terminal alpha helices in facilitating these processes. The deletion of these domains led to a progressive reduction in the affinity between SRP54 and FtsY, disrupting TC formation and compromising its catalytic efficiency. Molecular dynamics simulations and thermodynamic analyses corroborated these experimental findings, revealing that the A domain is integral to stabilizing TC and enhancing reciprocal GTP hydrolysis. Furthermore, the study showed that membrane association, mediated by the orientation of the A domain and the αN1 helix, is essential for stabilizing the interaction between SRP and the membrane. These results shed light on the molecular basis of SRP assembly and membrane targeting in archaea, marking an important advancement in our understanding of the archaeal SRP machinery.

Pig jejunal single-cell RNA landscapes revealing breed-specific immunology differentiation at various domestication stages

Background

Domestication of wild boars into local and intensive pig breeds has driven adaptive genomic changes, resulting in significant phenotypic differences in intestinal immune function. The intestine relies on diverse immune cells, but their evolutionary changes during domestication remain poorly understood at single-cell resolution.

Methods

We performed single-cell RNA sequencing (scRNA-seq) and marker gene analysis on jejunal tissues from wild boars, a Chinese local breed (Jinhua), and an intensive breed (Duroc). Then, we developed an immune cell evaluation system that includes immune scoring, gene identification, and cell communication analysis. Additionally, we mapped domestication-related clustering relationships, highlighting changes in gene expression and immune function.

Results

We generated a single-cell atlas of jejunal tissues, analyzing 26,246 cells and identifying 11 distinct cell lineages, including epithelial and plasma cells, and discovered shared and unique patterns in intestinal nutrition and immunity across breeds. Immune cell evaluation analysis confirmed the conservation and heterogeneity of immune cells, manifested by highly conserved functions of immune cell subgroups, but wild boars possess stronger immune capabilities than domesticated breeds. We also discovered four patterns of domestication-related breed-specific genes related to metabolism, immune surveillance, and cytotoxic functions. Lastly, we identified a unique population of plasma cells with distinctive antibody production in Jinhua pig population.

Conclusions

Our findings provide valuable single-cell insights into the cellular heterogeneity and immune function evolution in the jejunum during pig at various domestication stages. The single-cell atlas also serves as a resource for comparative studies and supports breeding programs aimed at enhancing immune traits in pigs.

Mechanistic Insights into Protein Biogenesis and Maturation on the Ribosome

The ribosome is a major cellular machine that converts genetic information into biological function. Emerging data show that the ribosome is not only a protein synthesis machine, but also participates in the maturation of the nascent protein into properly folded and active molecules. The ribosome surface near the opening of the polypeptide exit tunnel can interact directly with the newly synthesized proteins and, more importantly, provides a platform where numerous protein biogenesis factors assemble, gain access to the nascent chain, and direct them into diverse biogenesis pathways. In this article, we review the current understanding of cotranslational protein maturation pathways, with an emphasis on systems in which biochemical studies provided a high-resolution molecular understanding and yielded generalizable mechanistic principles.

A Trivalent Live Vaccine Elicits Cross-Species Protection Against Acute Otitis Media in a Murine Model

Background: Acute otitis media (AOM) is a common pediatric infection worldwide and is the primary basis for pediatric primary care visits and antibiotic prescriptions in children. Current licensed vaccines have been incompletely ineffective at reducing the global burden of AOM, underscoring a major unmet medical need. The complex etiology of AOM presents additional challenges for vaccine development, as it can stem from multiple bacterial species including Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis. As such, targeting multiple pathogens simultaneously may be required to significantly impact the overall disease burden. Methods: In this study, we aim to overcome this challenge by engineering a live-attenuated vaccine platform based on an attenuated mutant of S. pneumoniae that expresses H. influenzae and M. catarrhalis surface epitopes to induce protective immunity against all three pathogens. Results: The trivalent live-attenuated vaccine conferred significant protection against all three bacterial otopathogens as measured by seroconversion and the development of AOM, with the inclusion of the additional epitopes providing unexpected synergy and enhanced protection against S. pneumoniae. Conclusions: These data demonstrate a novel mechanism of introducing non-native immunogenic antigens into a live-attenuated vaccine platform to engender protection against AOM from multiple pathogenic species.

The viable but non-culturable (VBNC) status of Shewanella putrefaciens (S. putrefaciens) with thermosonication (TS) treatment

Although thermosonication (TS) treatment has been widely used in food sterilization, the viable but non-culturable (VBNC) of bacteria with TS treatment has still concerned potential food safety and public health. The molecular mechanism of VBNC status of bacteria with TS treatment is not clearly known. Therefore, in this study, we used Shewanella putrefaciens, which was a common putrefactive bacteria in aquatic products, to study the VBNC state of bacteria with TS treatment. Firstly, our results revealed that S. putrefaciens still could enter the VBNC state after TS treatments: 50 kHz, 300 W, 30 min ultrasonic treatment and 70 °C heating; Subsequently, we found the VBNC state of S. putrefaciens can resist the damage of TS treatment, such as cell wall break, DNA degradation, etc; Finally, four-dimensional data-independent acquisition-based proteomics showed that under VBNC state, S. putrefaciens upregulated functional proteins to resist TS treatment, such as: ribosomal proteins to accelerate the synthesis of stress proteins to counteract TS treatments, ornithine decarboxylase SpeF and MraY to repair TS treatment-induced damage, etc. Meanwhile, S. putrefaciens downregulates metabolic and transport functional proteins such as dehydrogenase to reduce the metabolism. Importantly, among those proteins, the ribosomal transcriptional regulatory protein family, such as rpsB, etc, may be the key proteins for S. putrefaciens entering VBNC state. This finding can provide some new strategies for preventing VBNC status of bacteria with TS treatment, such as: inhibition of key proteins, etc.

The metabolic basis of inherited neutropenias

Neutrophils are the shortest-lived blood cells, which requires a prodigious degree of proliferation and differentiation to sustain physiologically sufficient numbers and be poised to respond quickly to infectious emergencies. More than 107 neutrophils are produced every minute in an adult bone marrow-a process that is tightly regulated by a small group of cytokines and chemical mediators and dependent on nutrients and energy. Like granulocyte colony-stimulating factor, the primary growth factor for granulopoiesis, they stimulate signalling pathways, some affecting metabolism. Nutrient or energy deficiency stresses the survival, proliferation, and differentiation of neutrophils and their precursors. Thus, it is not surprising that monogenic disorders related to metabolism exist that result in neutropenia. Among these are pathogenic mutations in HAX1, G6PC3, SLC37A4, TAFAZZIN, SBDS, EFL1 and the mitochondrial disorders. These mutations perturb carbohydrate, lipid and/or protein metabolism. We hypothesize that metabolic disturbances may drive the pathogenesis of a subset of inherited neutropenias just as defects in DNA damage response do in Fanconi anaemia, telomere maintenance in dyskeratosis congenita and ribosome formation in Diamond-Blackfan anaemia. Greater understanding of metabolic pathways in granulopoiesis will identify points of vulnerability in production and may point to new strategies for the treatment of neutropenias.

Fidelity of Cotranslational Protein Targeting to the Endoplasmic Reticulum

Fidelity of protein targeting is essential for the proper biogenesis and functioning of organelles. Unlike replication, transcription and translation processes, in which multiple mechanisms to recognize and reject noncognate substrates are established in energetic and molecular detail, the mechanisms by which cells achieve a high fidelity in protein localization remain incompletely understood. Signal recognition particle (SRP), a conserved pathway to mediate the localization of membrane and secretory proteins to the appropriate cellular membrane, provides a paradigm to understand the molecular basis of protein localization in the cell. In this chapter, we review recent progress in deciphering the molecular mechanisms and substrate selection of the mammalian SRP pathway, with an emphasis on the key role of the cotranslational chaperone NAC in preventing protein mistargeting to the ER and in ensuring the organelle specificity of protein localization.

Molecular mechanism of cargo recognition and handover by the mammalian signal recognition particle

Co-translational protein targeting to membranes by the signal recognition particle (SRP) is a universally conserved pathway from bacteria to humans. In mammals, SRP and its receptor (SR) have many additional RNA features and protein components compared to the bacterial system, which were recently shown to play regulatory roles. Due to its complexity, the mammalian SRP targeting process is mechanistically not well understood. In particular, it is not clear how SRP recognizes translating ribosomes with exposed signal sequences and how the GTPase activity of SRP and SR is regulated. Here, we present electron cryo-microscopy structures of SRP and SRP·SR in complex with the translating ribosome. The structures reveal the specific molecular interactions between SRP and the emerging signal sequence and the elements that regulate GTPase activity of SRP·SR. Our results suggest the molecular mechanism of how eukaryote-specific elements regulate the early and late stages of SRP-dependent protein targeting.

Jomaa et al. present cryo-EM structures of mammalian SRP, SRP receptor, and the translating ribosome. The structures reveal the role of eukaryotic-specific features involved in regulating early and late stages of co-translational protein targeting to the endoplasmic reticulum and suggest a model for cargo recognition and handover.

Direct observation of alpha-lactalbumin, adsorption and incorporation into lipid membrane and formation of lipid/protein hybrid structures

The interaction between proteins and membranes is of great interest in biomedical and biotechnological research for its implication in many functional and dysfunctional processes. We present an experimental study on the interaction between model membranes and alpha-lactalbumin (α-La). α-La is widely studied for both its biological function and its anti-tumoral properties. We use advanced fluorescence microscopy and spectroscopy techniques to characterize α-La-membrane mechanisms of interaction and α-La-induced modifications of membranes when insertion of partially disordered regions of protein chains in the lipid bilayer is favored. Moreover, using fluorescence lifetime imaging, we are able to distinguish between protein adsorption and insertion in the membranes. Our results indicate that, upon addition of α-La to giant vesicles samples, protein is inserted into the lipid bilayer with rates that are concentration-dependent. The formation of heterogeneous hybrid protein-lipid co-aggregates, paralleled with protein conformational and structural changes, alters the membrane structure and morphology, leading to an increase in membrane fluidity.

Specific structural elements of the T-box riboswitch drive the two-step binding of the tRNA ligand

T-box riboswitches are cis-regulatory RNA elements that regulate the expression of proteins involved in amino acid biosynthesis and transport by binding to specific tRNAs and sensing their aminoacylation state. While the T-box modular structural elements that recognize different parts of a tRNA have been identified, the kinetic trajectory describing how these interactions are established temporally remains unclear. Using smFRET, we demonstrate that tRNA binds to the riboswitch in two steps, first anticodon recognition followed by the sensing of the 3’ NCCA end, with the second step accompanied by a T-box riboswitch conformational change. Studies on site-specific mutants highlight that specific T-box structural elements drive the two-step binding process in a modular fashion. Our results set up a kinetic framework describing tRNA binding by T-box riboswitches, and suggest such binding mechanism is kinetically beneficial for efficient, co-transcriptional recognition of the cognate tRNA ligand.

Living organisms depend upon a group of chemicals called amino acids to survive. Amino acids are the building blocks of proteins, and proteins have many important roles within and around cells. Bacteria regulate certain genes to ensure they have the right balance of different amino acids to survive. By controlling the availability of certain proteins that help them to make or collect certain amino acids, bacteria can control their overall amino acid balance.

Before a protein is made, a molecular machine called RNA polymerase must first copy the information in a gene to make a molecule called a messenger RNA (mRNA). The mRNA is then translated to make the protein from individual amino acids. In this process, each amino acid needs to be first attached to another molecule called a transfer RNA (tRNA). In many bacteria species, the mRNAs involved in making or transporting amino acids contain structures called T-boxes. These structures guide the RNA polymerase to make more of the mRNAs when the levels of the amino acid become too low. A T-box, however, does not sense the level of the amino acid directly. Instead it senses the number of tRNA molecules that do not carry an amino acid.

Zhang, Chetnani et al. examined a particular T-box interacting with tRNA using pairs of fluorescent dyes to detect distances between molecules. The T-box first recognizes a part of the tRNA called the anticodon to make sure it binds the correct type of tRNA. It then changes its shape to detect whether the tRNA is attached to an amino acid. This two-step process is driven by multiple structural elements within the T-box, and the flexibility of the T-box plays a critical role.

A cell’s survival depends on it keeping amino acid levels under control. Understanding how bacteria do this could lead to new antibiotic drugs that target the T-box to kill cells. This study also provides insights into the workings of mRNA components like T-boxes – a type of riboswitch – which is an unusual means of controlling gene activity.