SignalP 6.0 predicts all five types of signal peptides using protein language models

Signal peptides (SPs) are short amino acid sequences that control protein secretion and translocation in all living organisms. SPs can be predicted from sequence data, but existing algorithms are unable to detect all known types of SPs. We introduce SignalP 6.0, a machine learning model that detects all five SP types and is applicable to metagenomic data.

Physicochemical, Oxidative Stability and Sensory Properties of Frankfurter-Type Sausage as Influenced by the Addition of Carrot (Daucus carota) Paste

This study examined the addition of carrot paste (CP) at levels of 3%, 5%, and 10% as a potential antioxidant in frankfurter-type sausages, denoted as F1, F2, and F3. F0, was a control sample with no addition of CP. All formulated samples were stored for 14 days during which their physicochemical, oxidative stability, and sensory properties were evaluated. Results showed that the pH of frankfurter-type sausages was not affected by the addition of CP, however, higher pH values were observed in CP-enriched samples on the first day of production and subsequent storage days. Cooking loss (CL) in frankfurter-type sausages was in the range of 2.20% to 2.87%, with the CP-enriched samples having a lower CL percentage, particularly F3 samples, compared to the control. Protein and fat content were lower in CP-enriched samples, but ash content increased. CP-enriched frankfurter-type sausages recorded significantly higher polyphenol contents compared to the control. Total polyphenol content in CP-enriched samples F1, F2, and F3 was higher throughout storage compared to the control. Lower peroxide values were also recorded in CP-enriched samples F1 (2.5 meq/kg), F2 (2.4 meq/kg), and F3 (2.2 meq/kg) compared to the control (2.9 meq/kg), demonstrating greater 2,2-Diphenyl-1-picrylhydrazyl (DPPH) antioxidant activity than the control samples. Formulations treated with 10% CP gained significantly higher scores for color, texture, and overall acceptability. Principal component analysis showed that higher inclusion levels of CP in formulation improved the sensory quality and oxidative stability. In conclusion, CP could be used to enhance the oxidative stability of frankfurter-type sausage without negatively influencing the sensory quality.

Toxoplasma gondii phosphatidylserine flippase complex ATP2B-CDC50.4 critically participates in microneme exocytosis

Regulated microneme secretion governs motility, host cell invasion and egress in the obligate intracellular apicomplexans. Intracellular calcium oscillations and phospholipid dynamics critically regulate micronemes exocytosis. Despite its importance for the lytic cycle of these parasites, molecular mechanistic details about exocytosis are still missing. Some members of the P4-ATPases act as flippases, changing the phospholipid distribution by translocation from the outer to the inner leaflet of the membrane. Here, the localization and function of the repertoire of P4-ATPases was investigated across the lytic cycle of Toxoplasma gondii. Of relevance, ATP2B and the non-catalytic subunit cell division control protein 50.4 (CDC50.4) form a stable heterocomplex at the parasite plasma membrane, essential for microneme exocytosis. This complex is responsible for flipping phosphatidylserine (PS), which presumably acts as a lipid mediator for the organelle fusion with the plasma membrane. DOC2.1, a previously described key egress and invasion factor, is shown here to be affected in its function in egress upon mutation on residues putatively involved in calcium binding. This study points toward the importance of PS in microneme exocytosis and unveils subtle differences in the signaling cascades leading to organelle secretion between intracellular and extracellular parasites to ensure egress and invasion, respectively.

An improved auxin-inducible degron system for fission yeast

Conditional degron technologies, which allow a protein of interest to be degraded in an inducible manner, are important tools for biological research, and are especially useful for creating conditional loss-of-function mutants of essential genes. The auxin-inducible degron (AID) technology, which utilizes plant auxin signaling components to control protein degradation in nonplant species, is a widely used small-molecular-controlled degradation method in yeasts and animals. However, the currently available AID systems still have room for further optimization. Here, we have improved the AID system for the fission yeast Schizosaccharomyces pombe by optimizing all three components: the AID degron, the small-molecule inducer, and the inducer-responsive F-box protein. We chose a 36-amino-acid sequence of the Arabidopsis IAA17 protein as the degron and employed three tandem copies of it to enhance efficiency. To minimize undesirable side effects of the inducer, we adopted a bulky analog of auxin, 5-adamantyl-IAA, and paired it with the F-box protein OsTIR1 that harbors a mutation (F74A) at the auxin-binding pocket. 5-adamantyl-IAA, when utilized with OsTIR1-F74A, is effective at concentrations thousands of times lower than auxin used in combination with wild-type OsTIR1. We tested our improved AID system on 10 essential genes and achieved inducible lethality for all of them, including ones that could not be effectively inactivated using a previously published AID system. Our improved AID system should facilitate the construction of conditional loss-of-function mutants in fission yeast.

Transcriptome Analysis Reveals Catabolite Control Protein A Regulatory Mechanisms Underlying Glucose-Excess or -Limited Conditions in a Ruminal Bacterium, Streptococcus bovis

Ruminants may suffer from rumen acidosis when fed with high-concentrate diets due to the higher proliferation and overproduction of lactate by Streptococcus bovis. The catabolite control protein A (CcpA) regulates the transcription of lactate dehydrogenase (ldh) and pyruvate formate-lyase (pfl) in S. bovis, but its role in response to different carbon concentrations remains unclear. To characterize the regulatory mechanisms of CcpA in S. bovis S1 at different levels of carbon, herein, we analyzed the transcriptomic and physiological characteristics of S. bovis S1 and its ccpA mutant strain grown in glucose-excess and glucose-limited conditions. A reduced growth rate and a shift in fermentation pattern from homofermentation to heterofermentation were observed under glucose-limited condition as compared to glucose-excess condition, in S. bovis S1. Additionally, the inactivation of ccpA significantly affected the growth and end metabolites in both conditions. For the glycolytic intermediate, fructose 1,6-bisphosphate (FBP), the concentration significantly reduced at lower glucose conditions; its concentration decreased significantly in the ccpA mutant strain. Transcriptomic results showed that about 46% of the total genes were differentially transcribed between the wild-type strain and ccpA mutant strain grown in glucose-excess conditions; while only 12% genes were differentially transcribed in glucose-limited conditions. Different glucose concentrations led to the differential expression of 38% genes in the wild-type strain, while only half of these were differentially expressed in the ccpA-knockout strain. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that the substrate glucose concentration significantly affected the gene expression in histidine metabolism, nitrogen metabolism, and some carbohydrate metabolism pathways. The deletion of ccpA affected several genes involved in carbohydrate metabolism, such as glycolysis, pyruvate metabolism, fructose and mannose metabolism, as well as in fatty acid biosynthesis pathways in bacteria grown in glucose-excess conditions; this effect was attenuated under glucose-limited conditions. Overall, these findings provide new information on gene transcription and metabolic mechanisms associated with substrate glucose concentration and validate the important role of CcpA in the regulation of carbon metabolism in S. bovis S1 at differential glucose availability.

Growth of Pancreas and Intestinal Enzyme Activities in Growing Goats: Influence of a Low-Protein Diet

A dependence between dietary protein and starch levels flowing to the duodenum has been characterized in monogastric animals for optimal enzymatic secretions of the pancreas, but those in ruminants remain unclarified. The present experiment was conveyed to assess the pancreas growth and mRNA expression of the small intestine enzymes in growing goats fed a low-protein diet. Twenty-four Liuyang goats (19.55 ± 3.55 of body weight (BW)) and aged approximately 8 months were randomly assigned to either a control protein diet (NP: 10.77% CP) or a low-protein diet (LP: 5.52% CP) for 70 days. The results show that no statistical differences (p > 0.05) were observed in the pancreas growth indices between the groups. Pancreas and small intestine α-amylase and lipase activities were unaffected (p > 0.05) by the LP diet, while activities of trypsin and chymotrypsin were decreased (p < 0.05). The LP diet reduced (p < 0.05) the mRNA expressions of trypsin and chymotrypsin in the duodenum and jejunum, and had no effects (p > 0.05) on the mRNA expressions of α-amylase and lipase. Goats fed with the LP diet had higher (p < 0.05) concentrations of cholecystokinin and insulin than those fed with the NP diet. In conclusion, feeding an LP diet (5.52% CP) had no profound influence on pancreas growth and digestive enzyme synthesis in goats.

Cell Division Control Protein 42 Interacts With Hepatitis E Virus Capsid Protein and Participates in Hepatitis E Virus Infection

Hepatitis E Virus (HEV) causes viral hepatitis in humans worldwide, while a subset of HEV species, avian HEV, causes hepatitis-splenomegaly syndrome in chickens. To date, there are few reports on the host proteins interacting with HEV and being involved in viral infection. Previous pull-down assay combining mass spectrometry indicated that cell division control protein 42 (CDC42), a member belonging to the Rho GTPase family, was pulled down by avian HEV capsid protein. We confirmed the direct interaction between CDC42 and avian and mammalian HEV capsid proteins. The interaction can increase the amount of active guanosine triphosphate binding CDC42 state (GTP-CDC42). Subsequently, we determined that the expression and activity of CDC42 were positively correlated with HEV infection in the host cells. Using the different inhibitors of CDC42 downstream signaling pathways, we found that CDC42-MRCK (a CDC42-binding kinase)-non-myosin IIA (NMIIA) pathway is involved in naked avian and mammalian HEV infection, CDC42-associated p21-activated kinase 1 (PAK1)-NMIIA/Cofilin pathway is involved in quasi-enveloped mammalian HEV infection and CDC42-neural Wiskott-Aldrich syndrome protein-actin-polymerizing protein Arp2/3 pathway (CDC42-(N-)WASP-Arp2/3) pathway participates in naked and quasi-enveloped mammalian HEV infection. Collectively, these results demonstrated for the first time that HEV capsid protein can directly bind to CDC42, and non- and quasi-enveloped HEV use different CDC42 downstream signaling pathways to participate in viral infection. The study provided some new insights to understand the life cycle of HEV in host cells and a new target of drug design for combating HEV infection.