Atypical Pathway Research Articles

Advances in Plant Auxin Biology: Synthesis, Metabolism, Signaling, Interaction with Other Hormones, and Roles under Abiotic Stress.

Auxin is a key hormone that regulates plant growth and development, including plant shape and sensitivity to environmental changes. Auxin is biosynthesized and metabolized via many parallel pathways, and it is sensed and transduced by both normal and atypical pathways. The production, catabolism, and signal transduction pathways of auxin primarily govern its role in plant growth and development, and in the response to stress. Recent research has discovered that auxin not only responds to intrinsic developmental signals, but also mediates various environmental signals (e.g., drought, heavy metals, and temperature stresses) and interacts with hormones such as cytokinin, abscisic acid, gibberellin, and ethylene, all of which are involved in the regulation of plant growth and development, as well as the maintenance of homeostatic equilibrium in plant cells. In this review, we discuss the latest research on auxin types, biosynthesis and metabolism, polar transport, signaling pathways, and interactions with other hormones. We also summarize the important role of auxin in plants under abiotic stresses. These discussions provide new perspectives to understand the molecular mechanisms of auxin's functions in plant development.

Extracellular Overexpression of a Neutral Pullulanase in Bacillus subtilis through Multiple Copy Genome Integration and Atypical Secretion Pathway Enhancement.

Neutral pullulanases, having a good application prospect in trehalose production, showed a limited expression level. In order to address this issue, two approaches were utilized to enhance the yield of a new neutral pullulanase variant (PulA3E) in B. subtilis. One involved using multiple copies of genome integration to increase its expression level and fermentation stability. The other focused on enhancing the PulA-type atypical secretion pathway to further improve the secretory expression of PulA3E. Several strains with different numbers of genome integrations, ranging from one to four copies, were constructed. The four-copy genome integration strain PD showed the highest extracellular pullulanase activity. Additionally, the integration sites ytxE, ytrF, and trpP were selected based on their ability to enhance the PulA-type atypical secretion pathway. Furthermore, overexpressing the predicated regulatory genes comEA and yvbW of the PulA-type atypical secretion pathway in PD further improved its extracellular expression. Three-liter fermenter scale-up production of PD and PD-ARY yielded extracellular pullulanase activity of 1767.1 U/mL at 54 h and 2465.1 U/mL at 78 h, respectively. Finally, supplementing PulA3E with 40 U/g maltodextrin in the multi-enzyme catalyzed system resulted in the highest trehalose production of 166 g/L and the substrate conversion rate of 83%, indicating its potential for industrial application.

Metagenomic insights into Heimdallarchaeia clades from the deep-sea cold seep and hydrothermal vent

Heimdallarchaeia is a class of the Asgardarchaeota, are the most probable candidates for the archaeal protoeukaryote ancestor that have been identified to date. However, little is known about their life habits regardless of their ubiquitous distribution in diverse habitats, which is especially true for Heimdallarchaeia from deep-sea environments. In this study, we obtained 13 metagenome-assembled genomes (MAGs) of Heimdallarchaeia from the deep-sea cold seep and hydrothermal vent. These MAGs belonged to orders o_Heimdallarchaeales and o_JABLTI01, and most of them (9 MAGs) come from the family f_Heimdallarchaeaceae according to genome taxonomy database (GTDB). These are enriched for common eukaryote-specific signatures. Our results show that these Heimdallarchaeia have the metabolic potential to reduce sulfate (assimilatory) and nitrate (dissimilatory) to sulfide and ammonia, respectively, suggesting a previously unappreciated role in biogeochemical cycling. Furthermore, we find that they could perform both TCA and rTCA pathways coupled with pyruvate metabolism for energy conservation, fix CO2 and generate organic compounds through an atypical Wood-Ljungdahl pathway. In addition, many genes closely associated with bacteriochlorophyll and carotenoid biosynthesis, and oxygen-dependent metabolic pathways are identified in these Heimdallarchaeia MAGs, suggesting a potential light-utilization by pigments and microoxic lifestyle. Taken together, our results indicate that Heimdallarchaeia possess a mixotrophic lifestyle, which may give them more flexibility to adapt to the harsh deep-sea conditions.

The role of pyroptosis in heart failure and related traditional chinese medicine treatments.

Pyroptosis is a type of programmed cell death that is mediated by both typical and atypical pathways and ultimately leads to the lysis and rupture of cell membranes and the release of proinflammatory factors, triggering an intense inflammatory response. Heart failure (HF) is a serious and terminal stage of various heart diseases. Myocardial hypertrophy, myocardial fibrosis, ventricular remodeling, oxidative stress, the inflammatory response and cardiomyocyte ionic disorders caused by various cardiac diseases are all risk factors for and aggravate HF. Numerous studies have shown that pyroptosis can induce and exacerbate these reactions, causing progression to HF. Therefore, targeting pyroptosis is a promising strategy to treat HF. This paper summarizes the role of pyroptosis in the development of HF and the underlying mechanism involved. Recent research progress on the ability of traditional Chinese medicine (TCM) extracts and formulas to inhibit pyroptosis and treat HF was summarized, and some traditional Chinese medicine extracts and formulas can alleviate different types of HF, including heart failure with preserved ejection fraction (HFpEF), heart failure with reduced ejection fraction (HFrEF), and heart failure with midrange ejection fraction (HFmrEF), by targeting pyroptosis. These findings may provide new ideas and evidence for the treatment or adjuvant treatment of HF by targeting pyroptosis.

Insights into metastatic roadmap of head and neck cancer squamous cell carcinoma based on clinical, histopathological and molecular profiles.

The incidence of head and neck cancer (HNC), constituting approximately one in ten cancer cases worldwide, affects approximately 644,000 individuals annually. Managing this complex disease involves various treatment modalities such as systemic therapy, radiation, and surgery, particularly for patients with locally advanced disease. HNC treatment necessitates a multidisciplinary approach due to alterations in patients' genomes affecting their functionality. Predominantly, squamous cell carcinomas (SCCs), the majority of HNCs, arise from the upper aerodigestive tract epithelium. The epidemiology, staging, diagnosis, and management techniques of head and neck squamous cell carcinoma (HNSCC), encompassing clinical, image-based, histopathological and molecular profiling, have been extensively reviewed. Lymph node metastasis (LNM) is a well-known predictive factor for HNSCC that initiates metastasis and significantly impacts HNSCC prognosis. Distant metastasis (DM) in HNSCC has been correlated to aberrant expression of cancer cell-derived cytokines and growth factors triggering abnormal activation of several signaling pathways that boost cancer cell aggressiveness. Recent advances in genetic profiling, understanding tumor microenvironment, oligometastatic disease, and immunotherapy have revolutionized treatment strategies and disease control. Future research may leverage genomics and proteomics to identify biomarkers aiding individualized HNSCC treatment. Understanding the molecular basis, genetic landscape, atypical signaling pathways, and tumor microenvironment have enhanced the comprehension of HNSCC molecular etiology. This critical review sheds light on regional and distant metastases in HNSCC, presenting major clinical and laboratory features, predictive biomarkers, and available therapeutic approaches.

Fluoride induces pyroptosis via IL-17A-mediated caspase-1/11-dependent pathways and Bifidobacterium intervention in testis

Fluoride, a ubiquitous environmental pollutant, poses a significant public health threat. Our previous study revealed a correlation between fluoride-induced testicular pyroptosis and male reproductive dysfunction. However, the underlying mechanism remains unclear. Wild-type and interleukin 17A knockout mice were exposed to sodium fluoride (100 mg/L) in deionized drinking water for 18 weeks. Bifidobacterium intervention (1 × 109 CFU/mL, 0.2 mL/day, administered via gavage) commenced in the 10th week. Sperm quality, testicular morphology, key pyroptosis markers, spermatogenesis key genes, IL-17A signaling pathway, and pyroptosis pathway related genes were determined. The results showed that fluoride reduced sperm quality, damaged testicular morphology, affected spermatogenesis, elevated IL-17A levels, and induced testicular pyroptosis. Bifidobacterium intervention alleviated adverse reproductive outcomes. Fluoride-activated testicular pyroptosis through both typical and atypical pathways, with IL-17A involvement. Bifidobacterium supplementation attenuated pyroptosis by downregulating IL-17A, inhibiting NLRP3 and PYRIN-mediated caspase-1 and caspase-11 dependent pathways in testis, thereby alleviating fluoride-induced male reproductive damage. In summary, this study uncovers the mechanism underlying fluorine-induced testicular pyroptosis and illustrates the novel protecting feature of Bifidobacterium against fluoride-induced harm to male reproduction, along with its potential regulatory mechanism. These results provide fresh perspectives on treating male reproductive dysfunction resulting from fluoride or other environmental toxins.

Comment on “The ‘seed-fern’ Lepidopteris mass-produced the abnormal pollen Ricciisporites during the end-Triassic biotic crisis” by V. Vajda, S. McLoughlin, S. M. Slater, O. Gustafsson, and A. G. Rasmusson [Palaeogeography, Palaeoclimatology, Palaeoecology, 627 (2023), 111,723

Recently, Ricciisporites Lundblad and Cycadopites Wodehouse (=Monosulcites Cookson) pollen types have been found cooccurring in Antevsia zeilleri (Nathorst) Harris pollen sacs and it was assumed that the tetrads of Ricciisporites resulted from atypical pollen developmental pathway in which the pollen grains failed to separate. The pollen grains of Cycadopites type were interpreted as normal pollen grains of a peltasperm with Antevsia zeilleri pollen sacs and Lepidopteris ottonis (Göppert) Schimper foliage, and Ricciisporites, as abnormal pollen tetrads of this parent plant. However, if it were true, the exines in the pollen grains of the two types should have something in common in the ultrastructure. Examples of aberrant pollen in living seed plants show that changes occurring in the predetermined succession of events of exine development are minor and even if they finally lead to a significantly altered mature exine, the original structural plan remains recognizable. Contrariwise, the two pollen types are too dissimilar by their exine ultrastructure as well as by the general morphology and exine sculpture. Comparison with ontogenetic data on suitable modern analogues also allows one to suppose that exines of Ricciisporites and Cycadopites developed differently, in unrelated parent plants. Another explanation should be found for the presence of Ricciisporites tetrads in these pollen sacs.

Active prophages in coral-associated Halomonas capable of lateral transduction.

Temperate phages can interact with bacterial hosts through lytic and lysogenic cycles via different mechanisms. Lysogeny has been identified as the major form of bacteria-phage interaction in the coral-associated microbiome. However, the lysogenic-to-lytic switch of temperate phages in ecologically important coral-associated bacteria and its ecological impact have not been extensively investigated. By studying the prophages in coral-associated Halomonas meridiana, we found that two prophages, Phm1 and Phm3, are inducible by the DNA-damaging agent mitomycin C and that Phm3 is spontaneously activated under normal cultivation conditions. Furthermore, Phm3 undergoes an atypical lytic pathway that can amplify and package adjacent host DNA, potentially resulting in lateral transduction. The induction of Phm3 triggered a process of cell lysis accompanied by the formation of outer membrane vesicles (OMVs) and Phm3 attached to OMVs. This unique cell-lysis process was controlled by a four-gene lytic module within Phm3. Further analysis of the Tara Ocean dataset revealed that Phm3 represents a new group of temperate phages that are widely distributed and transcriptionally active in the ocean. Therefore, the combination of lateral transduction mediated by temperate phages and OMV transmission offers a versatile strategy for host-phage coevolution in marine ecosystems.

Unveiling the Dental Connection: A Case Report of Odontogenic Initiating Chronic Suppurative Otitis Media

ABSTRACT Chronic suppurative otitis media (CSOM) is a troubling condition that encompasses a range of factors contributing to its etiology. In this context, we present an intriguing and atypical case that adds a novel dimension to the understanding of CSOM. This particular case is marked by its prolonged and treatment-resistant nature, defying conventional medical treatments and prompting us to explore less common etiological pathways. Our case, however, deviates from the norm. It presents a conundrum that led us to investigate an alternative and less explored avenue. During our comprehensive diagnostic evaluation, our attention was drawn to the possibility of a hematogenic infection that may have originated from dental caries. This scenario emerged as the primary candidate for the source of the patient's chronic suppurative otitis media. This intriguing case represents a unique instance of a hematogenic infection stemming from dental caries. The hematogenic pathway, while previously considered uncommon, may be the precipitating factor behind the development of chronic suppurative otitis media in this patient. This perspective widens our understanding of the various potential etiological factors contributing to CSOM and highlights the importance of considering less conventional sources of infection. In the context of otologic disorders, the case we present underscores the necessity of a thorough and holistic diagnostic approach, acknowledging that the origins of such conditions can often be multifaceted and not limited to the conventional causes. Furthermore, this case serves as a reminder for clinicians to maintain a high level of suspicion for atypical etiological pathways when faced with treatment-resistant and persistent manifestations of CSOM. Keywords: Chronic Suppurative Otitis Media, Dental Caries, Odontogenic, Hematogenic

Research progress of chlorogenic acid in improving inflammatory diseases.

Long-term inflammation will develop into chronic inflammation and become inflammatory diseases. Antibiotics are commonly used in clinical practice to treat inflammatory diseases. But patients are prone to drug resistance. So we need to find new treatment. Chlorogenic acid is an organic compound extracted from honeysuckle and other plants. Its anti-inflammatory activity is strong, and it has a significant anti-inflammatory effect on inflammatory diseases in various systems. It has been shown that chlorogenic acid can regulate inflammation-related signaling pathways, such as nuclear factor κB (NF-κB) canonical signaling pathway, NF-κB atypical signaling pathway, nuclear factor-erythroid 2-related factor 2 (Nrf2) canonical signaling pathway, and Nrf2 atypical signaling pathway, etc. It can up-regulate the expression of anti-inflammatory cytokines such as interleukin (IL)-4, IL-10, IL-13 and down-regulate the expression of pro-inflammatory cytokine such as IL-1β, IL-6, and IL-8. Although chlorogenic acid has a strong anti-inflammatory effect, but clinical trials and application still face many difficulties. In the future, the anti-inflammatory molecular mechanism of chlorogenic acid should be further studied to explore its clinical application value and improve new ideas for the treatment of inflammatory diseases.

Kinetic characterization of annotated glycolytic enzymes present in cellulose-fermenting Clostridium thermocellum suggests different metabolic roles

BackgroundThe efficient production of sustainable biofuels is important for the reduction of greenhouse gas emissions. Clostridium thermocellum ATCC 27405 is a candidate for ethanol production from lignocellulosic biomass using consolidated bioprocessing. Fermentation of cellulosic biomass goes through an atypical glycolytic pathway in this thermophilic bacterium, with various glycolytic enzymes capable of utilizing different phosphate donors, including GTP and inorganic pyrophosphate (PPi), in addition to or in place of the usual ATP. C. thermocellum contains three annotated phosphofructokinases (PFK) genes, the expression of which have all been detected through proteomics and transcriptomics. Pfp (Cthe_0347) was previously characterized as pyrophosphate dependent with fructose-6-phosphate (F6P) as its substrate.ResultsWe now demonstrate that this enzyme can also phosphorylate sedoheptulose-7-phosphate (an intermediate in the pentose phosphate pathway), with the Vmax and Km of F6P being approximately 15 folds higher and 43 folds lower, respectively, in comparison to sedoheptulose-7-phosphate. Purified PfkA shows preference for GTP as the phosphate donor as opposed to ATP with a 12.5-fold difference in Km values while phosphorylating F6P. Allosteric regulation is a factor at play in PfkA activity, with F6P exhibiting positive cooperativity, and an apparent requirement for ammonium ions to attain maximal activity. Phosphoenolpyruvate and PPi were the only inhibitors for PfkA determined from the study, which corroborates what is known about enzymes from this subfamily. The activation or inhibition by these ligands lends support to the argument that glycolysis is regulated by metabolites such as PPi and NH4+ in the organism. PfkB, showed no activity with F6P, but had significant activity with fructose, while utilizing either ATP or GTP, making it a fructokinase. Rounding out the upper glycolysis pathway, the identity of the fructose-1,6-bisphosphate aldolase in the genome was verified and reported to have substantial activity with fructose-1,6-bisphosphate, in the presence of the divalent ion, Zn2+.ConclusionThese findings along with previous proteomic data suggest that Pfp, plays a role in both glycolysis and the pentose phosphate pathway, while PfkA and PfkB may phosphorylate sugars in glycolysis but is responsible for sugar metabolism elsewhere under conditions outside of growth on sufficient cellobiose.

Taxonomic and carbon metabolic diversification of Bathyarchaeia during its coevolution history with early Earth surface environment

Bathyarchaeia, as one of the most abundant microorganisms on Earth, play vital roles in the global carbon cycle. However, our understanding of their origin, evolution, and ecological functions remains poorly constrained. Here, we present the largest dataset of Bathyarchaeia metagenome assembled genome to date and reclassify Bathyarchaeia into eight order-level units corresponding to the former subgroup system. Highly diversified and versatile carbon metabolisms were found among different orders, particularly atypical C1 metabolic pathways, indicating that Bathyarchaeia represent overlooked important methylotrophs. Molecular dating results indicate that Bathyarchaeia diverged at ~3.3 billion years, followed by three major diversifications at ~3.0, ~2.5, and ~1.8 to 1.7 billion years, likely driven by continental emergence, growth, and intensive submarine volcanism, respectively. The lignin-degrading Bathyarchaeia clade emerged at ~300 million years perhaps contributed to the sharply decreased carbon sequestration rate during the Late Carboniferous period. The evolutionary history of Bathyarchaeia potentially has been shaped by geological forces, which, in turn, affected Earth’s surface environment.

Vascular variants in seed plants-a developmental perspective.

Over centuries of plant morphological research, biologists have enthusiastically explored how distinct vascular arrangements have diversified. These investigations have focused on the evolution of steles and secondary growth and examined the diversity of vascular tissues (xylem and phloem), including atypical developmental pathways generated through modifications to the typical development of ancestral ontogenies. A shared vernacular has evolved for communicating on the diversity of alternative ontogenies in seed plants. Botanists have traditionally used the term 'anomalous secondary growth' which was later renamed to 'cambial variants' by late Dr. Sherwin Carlquist (1988). However, the term 'cambial variants' can be vague in meaning since it is applied for developmental pathways that do not necessarily originate from cambial activity. Here, we review the 'cambial variants' concept and propose the term 'vascular variants' as a more inclusive overarching framework to interpret alternative vascular ontogenies in plants. In this framework, vascular variants are defined by their developmental origin (instead of anatomical patterns), allowing the classification of alternative vascular ontogenies into three categories: (i) procambial variants, (ii) cambial variants and (iii) ectopic cambia. Each category includes several anatomical patterns. Vascular variants, which represent broader developmental based groups, can be applied to both extant and fossil plants, and thereby offer a more adequate term from an evolutionary perspective. An overview of the developmental diversity and phylogenetic distribution of vascular variants across selected seed plants is provided. Finally, this viewpoint discusses the evolutionary implications of vascular variants.

Temporal trends of atypical drug access at an academic oncology unit: The Verona University Hospital experience.

e13651 Background: In Italy, patient (pt) access to oncological drugs is almost exclusively provided by the NHS, following authorization by the European Medicines Agency (EMA) and negotiation with the Italian Medicines Agency (AIFA) for specific indications. However, regulatory delays (with respect to the availability of scientific evidence) and the need for rapid access to innovative drugs, particularly in the context of orphan and rare diseases, have prompted the utilization of atypical drug access pathways. In addition to enrollment in clinical trials, atypical drug access pathways are expected to be increasingly used in the context of a Precision Oncology practice. Methods: We explored trends in atypical drug access at the Oncology Section of the Verona University and Hospital Trust, by interrogating Oncology and Pharmacy databases and regional registries of rare diseases and reviewing AIFA registries records. Data on atypical drug access were also correlated with the use of NGS-based molecular profiling. Results: Between January 2016 and December 2022, a total of 355 atypical drug access requests for the treatment of cancer pts were recorded, with a peak in 2017 and no discernible temporal trend. Over this period, the two most common atypical access schemes were compassionate (including named patient and early access programs, 61%) and off-label (21%) use. The latter steadily increased over time (from 8% in 2017 to 39% in 2021). Overall, the type of drugs requested through atypical access were almost equally distributed between classical cytotoxic agents (CHT, 36%), immuno-oncology drugs (IO, 29%) and molecularly targeted agents (TT, 35%). Temporal trends in the usage of different classes of drugs are shown. Interestingly, TT requests decreased between 2016 and 2018 and stabilized at approximately 50% of total requests since 2019. Between 2019 and 2021, atypical drug access requests triggered by NGS-based extended molecular profiling significantly increased from 2.8% to 23.1% (p=0.0007). Conclusions: Although atypical drug access did not increase overall during the observation period, a trend towards increased off-label use of TT was identified, especially from 2019 onwards; figures for 2022 are being analyzed and will be presented at the Meeting. Since 2019, NGS-informed requests have significantly increased to constitute almost 1/4 of all atypical drug access requests, clearly identifying a trend towards implementation of Precision Oncology in routine clinical practice and evolving towards the implementation of Molecular Tumor Board case discussions. [Table: see text]

A detailed genome-scale metabolic model of Clostridium thermocellum investigates sources of pyrophosphate for driving glycolysis

Lignocellulosic biomass is an abundant and renewable source of carbon for chemical manufacturing, yet it is cumbersome in conventional processes. A promising, and increasingly studied, candidate for lignocellulose bioprocessing is the thermophilic anaerobe Clostridium thermocellum given its potential to produce ethanol, organic acids, and hydrogen gas from lignocellulosic biomass under high substrate loading. Possessing an atypical glycolytic pathway which substitutes GTP or pyrophosphate (PPi) for ATP in some steps, including in the energy-investment phase, identification, and manipulation of PPi sources are key to engineering its metabolism. Previous efforts to identify the primary pyrophosphate have been unsuccessful. Here, we explore pyrophosphate metabolism through reconstructing, updating, and analyzing a new genome-scale stoichiometric model for C. thermocellum, iCTH669. Hundreds of changes to the former GEM, iCBI655, including correcting cofactor usages, addressing charge and elemental balance, standardizing biomass composition, and incorporating the latest experimental evidence led to a MEMOTE score improvement to 94%. We found agreement of iCTH669 model predictions across all available fermentation and biomass yield datasets. The feasibility of hundreds of PPi synthesis routes, newly identified and previously proposed, were assessed through the lens of the iCTH669 model including biomass synthesis, tRNA synthesis, newly identified sources, and previously proposed PPi-generating cycles. In all cases, the metabolic cost of PPi synthesis is at best equivalent to investment of one ATP suggesting no direct energetic advantage for the cofactor substitution in C. thermocellum. Even though no unique source of PPi could be gleaned by the model, by combining with gene expression data two most likely scenarios emerge. First, previously investigated PPi sources likely account for most PPi production in wild-type strains. Second, alternate metabolic routes as encoded by iCTH669 can collectively maintain PPi levels even when previously investigated synthesis cycles are disrupted. Model iCTH669 is available at github.com/maranasgroup/iCTH669.

IL-11 drives the phenotypic transformation of tracheal epithelial cells and fibroblasts to enhance abnormal repair after tracheal injury

Tracheal stenosis (TS) is a multifactorial and heterogeneous disease that can easily lead to respiratory failure and even death. Interleukin-11 (IL-11) has recently received increased attention as a fibrogenic factor, but its function in TS is uncertain. This study aimed to investigate the role of IL-11 in TS regulation based on clinical samples from patients with TS and a rat model of TS produced by nylon brush scraping. Using lentiviral vectors expressing shRNA (lentivirus-shRNA) targeting the IL-11 receptor (IL-11Rα), we lowered IL-11Rα levels in the rat trachea. Histological and immunostaining methods were used to evaluate the effects of IL-11Rα knockdown on tracheal injury, molecular phenotype, and fibrosis in TS rats. We show that IL-11 was significantly elevated in circulating serum and granulation tissue in patients with TS. In vitro, TGFβ1 dose-dependently stimulated IL-11 secretion from human tracheal epithelial cells (Beas-2b) and primary rat tracheal fibroblasts (PRTF). IL-11 transformed the epithelial cell phenotype to the mesenchymal cell phenotype by activating the β-catenin pathway. Furthermore, IL-11 activated the atypical ERK signaling pathway, stimulated fibroblasts proliferation, and transformed fibroblasts into alpha-smooth muscle actin (α-SMA) positive myofibroblasts. IL-11-neutralizing antibodies (IL-11NAb) or ERK inhibitors (U0126) inhibited IL-11 activity and downregulated fibrotic responses involving TGFβ/SMAD signaling. In vivo, IL-11Rα knockdown rats showed unobstructed tracheal lumen, relatively intact epithelial structure, and significantly reduced granulation tissue proliferation and collagen fiber deposition. Our findings confirm that IL-11 may be a target for future drug prevention and treatment of tracheal stenosis.

Overexpression of a Thermostable α-Amylase through Genome Integration in Bacillus subtilis

A carbohydrate binding module 68 (CBM68) of pullulanase from Anoxybacillus sp. LM18-11 was used to enhance the secretory expression of a thermostable α-amylase (BLA702) in Bacillus subtilis, through an atypical secretion pathway. The extracellular activity of BLA702 guided by CBM68 was 1248 U/mL, which was 12.6 and 7.2 times higher than that of BLA702 guided by its original signal peptide and the endogenous signal peptide LipA, respectively. A single gene knockout strain library containing 51 genes encoding macromolecular transporters was constructed to detect the effect of each transporter on the secretory expression of CBM68-BLA702. The gene knockout strain 0127 increased the extracellular amylase activity by 2.5 times. On this basis, an engineered strain B. subtilis 0127 (AmyE::BLA702-NprB::CBM68-BLA702-PrsA) was constructed by integrating BLA702 and CBM68-BLA702 at the AmyE and NprB sites in the genome of B. subtilis 0127, respectively. The molecular chaperone PrsA was overexpressed, to reduce the inclusion body formation of the recombinant enzymes. The highest extracellular amylase activity produced by B. subtilis 0127 (AmyE::BLA702-NprB::CBM68-BLA702-PrsA) was 3745.7 U/mL, which was a little lower than that (3825.4 U/mL) of B. subtilis 0127 (pMAC68-BLA702), but showing a better stability of passage. This newly constructed strain has potential for the industrial production of BLA702.

Exploring the Flexibility of the Glycopeptide Antibiotic Crosslinking Cascade for Extended Peptide Backbones.

The glycopeptide antibiotics (GPAs) are a clinically approved class of antimicrobial agents that classically function through the inhibition of bacterial cell-wall biosynthesis by sequestration of the precursor lipid II. The oxidative crosslinking of the core peptide by cytochrome P450 (Oxy) enzymes during GPA biosynthesis is both essential to their function and the source of their synthetic challenge. Thus, understanding the activity and selectivity of these Oxy enzymes is of key importance for the future engineering of this important compound class. Recent reports of GPAs that display an alternative mode of action and a wider range of core peptide structures compared to classic lipid II-binding GPAs raises the question of the tolerance of Oxy enzymes for larger changes in their peptide substrates. In this work, we explore the ability of Oxy enzymes from the biosynthesis pathways of lipid II-binding GPAs to accept altered peptide substrates based on a vancomycin template. Our results show that Oxy enzymes are more tolerant of changes at the N terminus of their substrates, whilst C-terminal extension of the peptide substrates is deleterious to the activity of all Oxy enzymes. Thus, future studies should prioritise the study of Oxy enzymes from atypical GPA biosynthesis pathways bearing C-terminal peptide extension to increase the substrate scope of these important cyclisation enzymes.

TGFβ3 regulates adipogenesis of bovine subcutaneous preadipocytes via typical Smad and atypical MAPK signaling pathways

BackgroundTransforming growth factor β3 (TGFβ3) is a member of TGFβ superfamily. Studies have shown that TGFβ is involved in adipose tissue biology. Whether TGFβ3 is a crucial regulator in adipogenic differentiation of bovine preadipocytes remains unclear. The main objective of this study was to investigate the effect of TGFβ3 on the adipogenic differentiation of bovine preadipocytes as well as the underlying mechanisms. ResultsPrimary subcutaneous preadipocytes derived from bovine subcutaneous adipose tissue were isolated and used as a cellular model. The results showed that TGFβ3 significantly promoted the proliferation of bovine preadipocytes and markedly decreased the lipid accumulation and expression levels of key adipogenic marker genes (PPARγ, c/EBPα, and FABP4) during adipocyte differentiation. In addition, TGFβ3 significantly increased the phosphorylation levels of Smad2, Smad3, JNK, and p38 in bovine preadipocytes, which could be eliminated by SB525334 (a TGFβRI inhibitor). Further studies showed that Smad3 and p38 mediated the inhibitory effect of TGFβ3 on differentiation, whereas Smad2 attenuated the anti-adipogenic effect of TGFβ3. ConclusionsTo sum up, our findings indicate that TGFβ3 is an important regulator of adipogenesis in bovine. TGFβ3 promotes the proliferation and regulates the differentiation of bovine preadipocytes through Smad2/3 and p38 signaling pathways.How to cite: Yang L, Wang H, Hao W, et al. TGFβ3 regulates adipogenesis of bovine subcutaneous preadipocytes via typical Smad and atypical MAPK signaling pathways. Electron J Biotechnol 2023;61. https://doi.org/10.1016/j.ejbt.2022.11.001.

An iron chlorophyll derivative for enhanced degradation of bisphenol A: New insight into the generation mechanism of high-valent iron oxo species

The pressure to environmental concern from toxic precursors of metalloporphyrin synthesis and the inadequate understanding of metalloporphyrin with β-site substituents on activation of peroxides have impeded the full potential of metalloporphyrin for the oxidation of recalcitrant organic compounds. Here, we report a “green” iron(III) chlorophyll derived from naturally abundant chlorophyll. It shows remarkable degradation efficiency of bisphenol A in the presence of hydrogen peroxide, with a second-order rate constant of 87.3 ± 1.1 L·mmol−1·min−1, which is 7-fold faster than the degradation rate of the Fenton oxidation system. It also demonstrates a wide pH tolerance range of 4–12 and is barely affected by concomitant inorganic anions or natural organic matter. Different from the generation of oxygen-centered radicals, including •OH and •O2−, in the Fenton system, a high-valent iron (Ⅳ) -oxo chlorin π-cation radical is formed with an atypical pathway of homolytic O O bond cleavage via a proton-coupled electron transfer process and is responsible for the degradation of bisphenol A, which is confirmed with spectroscopic studies and theoretical analysis. This abundant “green” catalyst could be beneficial for wastewater treatment by addressing the limitation of a narrow acidic pH range and the susceptibility to scavenging of nonselective radicals in conventional Fenton reactions.