Nanobodies combined with DNA-PAINT super-resolution reveal a staggered titin nanoarchitecture in flight muscles

Spatial transcriptomics in the adult Drosophila brain and body

Recently, we have achieved a significant milestone with the creation of the Fly Cell Atlas. This single-nuclei atlas encompasses the entire fly, covering the entire head and body, in addition to all major organs. This atlas catalogs many hundreds of cell types, of which we annotated 250. Thus, a large number of clusters remain to be fully characterized, in particular in the brain. Furthermore, by applying single-nuclei sequencing, all information about the spatial location of the cells in the body and of about possible subcellular localization of the mRNAs within these cells is lost. Spatial transcriptomics promises to tackle these issues. In a proof-of-concept study, we have here applied spatial transcriptomics using a selected gene panel to pinpoint the locations of 150 mRNA species in the adult fly. This enabled us to map unknown clusters identified in the Fly Cell Atlas to their spatial locations in the fly brain. Additionally, spatial transcriptomics discovered interesting principles of mRNA localization and transcriptional diversity within the large and crowded muscle cells that may spark future mechanistic investigations. Furthermore, we present a set of computational tools that will allow for easier integration of spatial transcriptomics and single-cell datasets.

Cu(II)-Dependent Spine Development Injury in Zebrafish (Danio rerio) with Organ Heterogeneous Cu Imbalance

Growing evidence suggests that the imbalance of Cu leads to multiorgan diseases or other adverse effects, but the underlying mechanisms remain largely unknown. Herein, we used zebrafish to uncover the mystery of organ heterogeneous responses to Cu stress and Cu(II)-dependent spine developmental injury in the early organogenesis stage. We first demonstrated that Cu(I) was distributed in the entire body, but high contents of Cu(II) were accumulated in the yolk sac and eye in normal zebrafish larvae. Cu exposure from birth to 144 hpf caused no obvious damage to Cu-metabolizing organs (liver and intestine), despite the elevated Cu(I) and Cu(II) levels. However, the spine was more sensitive to the Cu exposure. In the spine region, the Cu(I) level remained stable, whereas the level of Cu(II) significantly increased, which was highly associated with spine development injury. A significant negative correlation between Cu(II) and the spine-related parameters was identified. Moreover, cuproptosis caused spine development deformation during the early embryogenesis stage. Spine-related pathways such as somitegenesis significantly changed in the early embryogenesis period, and 5 spine-related pathways were significantly altered in the larval stage at 96 hpf. Our study suggested that Cu stress induced organ heterogeneous Cu imbalance and Cu(II)-dependent spine development injury in zebrafish.

Protein kinase 2 of the giant sarcomeric protein UNC-89 regulates mitochondrial morphology and function

UNC-89 is a giant sarcomeric M-line protein required for sarcomere organization and optimal muscle function. UNC-89 contains two protein kinase domains, PK1 and PK2, separated by an elastic region. Here we show that PK2 is a canonical kinase expected to be catalytically active. C. elegans expressing UNC-89 with a lysine to alanine (KtoA) mutation to inactivate PK2 have normally organized sarcomeres and SR, and normal muscle function. PK2 KtoA mutants have fragmented mitochondria, correlated with more mitochondrially-associated DRP-1. PK2 KtoA mutants have increased ATP levels, increased glycolysis and altered levels of electron transport chain complexes. Muscle mitochondria show increased complex I and decreased complex II basal respiration, each of which cannot be uncoupled. This suggests that mutant mitochondria are already uncoupled, possibly resulting from an increased level of the uncoupling protein, UCP-4. Our results suggest signaling from sarcomeres to mitochondria, to help match energy requirements with energy production.

Functionalized Protein Binders in Developmental Biology

Developmental biology has greatly profited from genetic and reverse genetic approaches to indirectly studying protein function. More recently, nanobodies and other protein binders derived from different synthetic scaffolds have been used to directly dissect protein function. Protein binders have been fused to functional domains, such as to lead to protein degradation, relocalization, visualization, or posttranslational modification of the target protein upon binding. The use of such functionalized protein binders has allowed the study of the proteome during development in an unprecedented manner. In the coming years, the advent of the computational design of protein binders, together with further advances in scaffold engineering and synthetic biology, will fuel the development of novel protein binder-based technologies. Studying the proteome with increased precision will contribute to a better understanding of the immense molecular complexities hidden in each step along the way to generate form and function during development.

Single molecule imaging unveils cellular architecture, dynamics and mechanobiology

The biomechanical regulation of the cytoskeleton and cell adhesions underlies various essential cellular functions. Studying them requires visualizing their nanostructure and molecular dynamics with evermore precise spatio-temporal resolution. In this review we will focus on the recent advances in single molecule fluorescence imaging techniques and discuss how they improve our understanding of mechanically sensitive cellular structures such as adhesions and the cytoskeleton. We will also discuss future directions for research, emphasizing on the 3D nature of cellular structures and tissues, their mechanical regulation at the molecule level, as well as how super-resolution microscopy will enhance our knowledge on protein structure and conformational changes in the cellular context.

An optimized approach to study nanoscale sarcomere structure utilizing super-resolution microscopy with nanobodies

The sarcomere is the fundamental contractile unit in skeletal muscle, and the regularity of its structure is critical for function. Emerging data demonstrates that nanoscale changes to the regularity of sarcomere structure can affect the overall function of the protein dense ~2μm sarcomere. Further, sarcomere structure is implicated in many clinical conditions of muscle weakness. However, our understanding of how sarcomere structure changes in disease, especially at the nanoscale, has been limited in part due to the inability to robustly detect and measure at sub-sarcomere resolution. We optimized several methodological steps and developed a robust pipeline to analyze sarcomere structure using structured illumination super-resolution microscopy in conjunction with commercially-available and fluorescently-conjugated Variable Heavy-Chain only fragment secondary antibodies (nanobodies), and achieved a significant increase in resolution of z-disc width (353nm vs. 62nm) compared to confocal microscopy. The combination of these methods provides a unique approach to probe sarcomere protein localization at the nanoscale and may prove advantageous for analysis of other cellular structures.

A novel strategy for an anti-idiotype vaccine: nanobody mimicking neutralization epitope of porcine circovirus type 2

Vaccination is the most effective method to protect humans and animals from diseases. Anti-idiotype vaccines are safer due to their absence of pathogens. However, the commercial production of traditional anti-idiotype vaccines using monoclonal and polyclonal antibodies (mAb and pAb) is complex and has a high failure rate. The present study designed a novel, simple, low-cost strategy for developing anti-idiotype vaccines with nanobody technology. We used porcine circovirus type 2 (PCV2) as a viral model, which can result in serious economic loss in the pig industry. The neutralizing mAb-1E7 (Ab1) against PCV2 capsid protein (PCV2-Cap) was immunized in the camel. And 12 nanobodies against mAb-1E7 were screened. Among them, Nb61 (Ab2) targeted the idiotype epitope of mAb-1E7 and blocked mAb-1E7's binding to PCV2-Cap. Additionally, a high-dose Nb61 vaccination can also protect mice and pigs from PCV2 infection. Epitope mapping showed that mAb-1E7 recognized the 75NINDFL80 of PCV2-Cap and 101NYNDFLG107 of Nb61. Subsequently, the mAb-3G4 (Ab3) against Nb61 was produced and can neutralize PCV2 infection in the PK-15 cells. Structure analysis showed that the amino acids of mAb-1E7 and mAb-3G4 respective binding to PCV2-Cap and Nb61 were also similar on the amino acids sequences and spatial conformation. Collectively, our study first provided a strategy for producing nanobody-based anti-idiotype vaccines and identified that anti-idiotype nanobodies could mimic the antigen on amino acids and structures. Importantly, as more and more neutralization mAbs against different pathogens are prepared, anti-idiotype nanobody vaccines can be easily produced against the disease with our strategy, especially for dangerous pathogens.IMPORTANCEAnti-idiotype vaccines utilize idiotype-anti-idiotype network theory, eliminating the need for external antigens as vaccine candidates. Especially for dangerous pathogens, they were safer because they did not contact the live pathogenic microorganisms. However, developing anti-idiotype vaccines with traditional monoclonal and polyclonal antibodies is complex and has a high failure rate. We present a novel, universal, simple, low-cost strategy for producing anti-idiotype vaccines with nanobody technology. Using a neutralization antibody against PCV2-Cap, a nanobody (Ab2) was successfully produced and could mimic the neutralizing epitope of PCV2-Cap. The nanobody can induce protective immune responses against PCV2 infection in mice and pigs. It highlighted that the anti-idiotype vaccine using nanobody has a very good application in the future, especially for dangerous pathogens.

The cryo-EM 3D image reconstruction of isolated Lethocerus indicus Z-discs

The Z-disk of striated muscle defines the ends of the sarcomere, which repeats many times within the muscle fiber. Here we report application of cryoelectron tomography and subtomogram averaging to Z-disks isolated from the flight muscles of the large waterbug Lethocerus indicus. We use high salt solutions to remove the myosin containing filaments and use gelsolin to remove the actin filaments of the A- and I-bands leaving only the thin filaments within the Z-disk which were then frozen for cryoelectron microscopy. The Lethocerus Z-disk structure is similar in many ways to the previously studied Z-disk of the honeybee Apis mellifera. At the corners of the unit cell are positioned trimers of paired antiparallel F-actins defining a large solvent channel, whereas at the trigonal positions are positioned F-actin trimers converging slowly towards their (+) ends defining a small solvent channel through the Z-disk. These near parallel F-actins terminate at different Z-heights within the Z-disk. The two types of solvent channel in Lethocerus are similar in size compared to those of Apis which are very different in size. Two types of α-actinin crosslinks were observed between oppositely oriented actin filaments. In one of these, the α-actinin long axis is almost parallel to the F-actins it crosslinks. In the other, the α-actinins are at a small but distinctive angle with respect to the crosslinked actin filaments. The utility of isolated Z-disks for structure determination is discussed.

A nanobody toolbox to investigate localisation and dynamics of Drosophila titins and other key sarcomeric proteins

Measuring the positions and dynamics of proteins in intact tissues or whole animals is key to understanding protein function. However, to date, this is challenging, as the accessibility of large antibodies to dense tissues is often limited, and fluorescent proteins inserted close to a domain of interest may affect protein function. These complications apply in particular to muscle sarcomeres, arguably one of the most protein-dense assemblies in nature, which complicates studying sarcomere morphogenesis at molecular resolution. Here, we introduce a toolbox of nanobodies recognising various domains of the two Drosophila titin homologs, Sallimus and Projectin, as well as the key sarcomeric proteins Obscurin, α-Actinin, and Zasp52. We verified the superior labelling qualities of our nanobodies in muscle tissue as compared to antibodies. By applying our toolbox to larval muscles, we found a gigantic Sallimus isoform stretching more than 2 µm to bridge the sarcomeric I-band, while Projectin covers almost the entire myosin filaments in a polar orientation. Transgenic expression of tagged nanobodies confirmed their high affinity-binding without affecting target protein function. Finally, adding a degradation signal to anti-Sallimus nanobodies suggested that it is difficult to fully degrade Sallimus in mature sarcomeres; however, expression of these nanobodies caused developmental lethality. These results may inspire the generation of similar toolboxes for other large protein complexes in Drosophila or mammals.