Signal Sequence Research Articles

Spc2 modulates substrate- and cleavage site-selection in the yeast signal peptidase complex.

Secretory proteins are critically dependent on the correct processing of their signal sequence by the signal peptidase complex (SPC). This step, which is essential for the proper folding and localization of proteins in eukaryotic cells, is still not fully understood. In eukaryotes, the SPC comprises four evolutionarily conserved membrane subunits (Spc1-3 and Sec11). Here, we investigated the role of Spc2, examining SPC cleavage efficiency on various models and natural signal sequences in yeast cells depleted of or with mutations in Spc2. Our data show that discrimination between substrates and identification of the cleavage site by SPC is compromised when Spc2 is absent or mutated. Molecular dynamics simulation of the yeast SPC AlphaFold2-Multimer model indicates that membrane thinning at the center of SPC is reduced without Spc2, suggesting a molecular explanation for the altered substrate recognition properties of SPC lacking Spc2. These results provide new insights into the molecular mechanisms by which SPC governs protein biogenesis.

KPNA3 regulates histone locus body formation by modulating condensation and nuclear import of NPAT.

The histone locus body (HLB) is a membraneless organelle that determines the transcription of replication-dependent histones. However, the mechanisms underlying the appropriate formation of the HLB in the nucleus but not in the cytoplasm remain unknown. HLB formation is dependent on the scaffold protein NPAT. We identify KPNA3 as a specific importin that drives the nuclear import of NPAT by binding to the nuclear localization signal (NLS) sequence. NPAT undergoes phase separation, which is inhibited by KPNA3-mediated impairment of self-association. In this, a C-terminal self-interaction facilitator (C-SIF) motif, proximal to the NLS, binds the middle 431-1,030 sequence to mediate the self-association of NPAT. Mechanistically, the anchoring of KPNA3 to the NPAT-NLS sterically blocks C-SIF motif-dependent NPAT self-association. This leads to the suppression of aberrant NPAT condensation in the cytoplasm. Collectively, our study reveals a previously unappreciated role of KPNA3 in modulating HLB formation and delineates a steric hindrance mechanism that prevents inappropriate cytoplasmic NPAT condensation.

C-repeat binding factor (CBF) identification and expression pattern to abiotic stress response in Casuarina equisetifolia and overexpression of CeCBF4 increase stress tolerance in Arabidopsis

Casuarina equisetifolia stands out as a highly valuable tree species crucial for industries and ecological restoration projects in tropical and subtropical regions, owing to its exceptional salt resistance. However, its growth is hampered in cold and drought-prone areas. Understanding the genetic basis for abiotic stress tolerance is imperative for enhancing stress-resistant breeding efforts of C. equisetifolia. However, the CBF genes are renowned for their pivotal roles in cold response and broad resilience to other adverse environments, such as drought, and high salinity. In this study, five CeCBFs were identified from the genome of C. equisetifolia. CeCBF1 and CeCBF3 belong to Clade I group, which diverged early from DREBIII members, while CeCBF2, CeCBF4, and CeCBF5 are classified into Clade II, a group innovated from Clade I. These genes lack introns in their sequences. The proteins encoded by CeCBFs feature classic AP2 domains and CBF signature sequences, localize in the nucleus and exhibit transactivation activity. Additionally, stress-related, abscisic acid, and jasmonic acid responsive elements are present on the CeCBFs promoters. Expression analysis revealed that CeCBFs were prodominantly induced by cold, drought, and salinity treatments, except for CeCBF1, which showed repression specifically under low temperature. Moreover, CeCBF1, CeCBF4, and CeCBF5 were inhibited by abscisic acid, while CeCBF1 showed reduced transcript levels in response to methyl jasmonate treatment. Furthermore, overexpression of CeCBF4 enhanced tolerance to low temperature, depriving of water, and salt by up-regulating stress-responsive genes expression and promoting proline accumulation, albeit with a trade-off in growth and productivity. Hence, CeCBFs emerge as potential regulators contributing significantly to stress tolerance mechanisms in C. equisetifolia.

Legionella pneumophila IrsA, a novel, iron-regulated exoprotein that facilitates growth in low-iron conditions and modulates biofilm formation.

To discover new factors that are involved in iron acquisition by Legionella pneumophila, we used RNA-Seq to identify the genes that are most highly induced when virulent strain 130b is cultured in a low-iron chemically defined medium. Among other things, this revealed 14915, a heretofore uncharacterized gene that is predicted to be transcriptionally regulated by Fur and to encode a novel, ~15 kDa protein. 14915 was present in all L. pneumophila strains examined and had homologs in a subset of the other Legionella species. Compatible with it containing a classic signal sequence, the 14915 protein was detected in bacterial culture supernatants in a manner dependent upon the L. pneumophila type II secretion system. Thus, we designated 14915 as IrsA for iron-regulated, secreted protein A. Based on mutant analysis, the irsA gene was not required for optimal growth of strain 130b in low-iron media. However, after discovering that the commonly used laboratory-derived strain Lp02 has a much greater requirement for iron, we uncovered a growth-enhancing role for IrsA after examining an Lp02 mutant that lacked both IrsA and the Fe2+-transporter FeoB. The irsA mutant of 130b, but not its complemented derivative, did, however, display increased biofilm formation on both plastic and agar surfaces, and compatible with this, the mutant hyper-aggregated. Thus, IrsA is a novel, iron-regulated exoprotein that modulates biofilm formation and, under some circumstances, promotes growth in low-iron conditions. For this study, we determined and deposited in the database a complete and fully assembled genome sequence for strain 130b.IMPORTANCEThe bacterium Legionella pneumophila is the principal cause of Legionnaires' disease, a potentially fatal form of pneumonia that is increasing in incidence. L. pneumophila exists in many natural and human-made water systems and can be transmitted to humans through inhalation of contaminated water droplets. L. pneumophila flourishes within its habitats by spreading planktonically, assembling into biofilms, and growing in larger host cells. Iron acquisition is a key determinant for L. pneumophila persistence in water and during infection. We previously demonstrated that L. pneumophila assimilates iron both by secreting a non-protein iron chelator (siderophore) and by importing iron through membrane transporters. In this study, we uncovered a novel, secreted protein that is highly iron-regulated, promotes L. pneumophila's growth in low-iron media, and impacts biofilm formation. We also identified uncharacterized, IrsA-related proteins in other important human and animal pathogens. Thus, our results have important implications for understanding iron assimilation, biofilm formation, and pathogenesis.

A widespread accessory protein family diversifies the effector repertoire of the type VI secretion system spike

Type VI secretion systems (T6SSs) are macromolecular assemblies that deliver toxic effector proteins between adjacent bacteria. These effectors span a wide range of protein families that all lack canonical signal sequences that would target them for export. Consequently, it remains incompletely understood how conserved structural components of the T6SS apparatus recognize a diverse repertoire of effectors. Here, we characterize a widespread family of adaptor proteins, containing the domain of unknown function DUF4123, that enable the recognition and export of evolutionarily unrelated effectors. By examining two nearly identical paralogs of the conserved T6SS spike protein, VgrG, we demonstrate that each spike protein exports a structurally unique effector. We further show that the recruitment of each effector to its respective spike protein requires a cognate adaptor protein. Protein–protein interaction experiments demonstrate that these adaptor proteins specifically tether an effector to a structurally conserved but sequence divergent helix-turn-helix motif found at the C-terminus of its cognate VgrG. Using structural predictions and mutagenesis analyses, we elucidate the molecular contacts required for these interactions and discover that these adaptor proteins contain a structurally conserved N-terminal lobe that has evolved to bind VgrG helix-turn-helix motifs and a structurally variable C-terminal lobe that recognizes diverse effector families. Overall, our work provides molecular insight into a mechanism by which conserved T6SS components recognize structurally diverse effectors.

Exploring secretory signal sequences useful in excreting recombinant proteins in Beauveria bassiana as biocontrol fungus.

Entomopathogenic fungi excrete a group of proteins to assimilate nutrients and defeat the host immune defense. Functional secretory signal sequences are needed for efficient secretion of the virulence-related proteins in recombinant strain. In this study, secretome analysis was used to explore the secreted proteins of Beauveria bassiana. Enrichment analysis indicated that B. bassiana secretome was mainly associated with metabolism of glucoside, polysaccharide, extracellular ester compound, and so on. In addition, proteins associated with biogenesis of cellular components were also enriched, including those involved in biogenesis of cell wall and vacuole. Then, four secretory signal sequences were functionally verified with green fluorescent protein as reporter. Finally, a signal sequence was used to excrete three insect venom protein serpins in B. bassiana, in which over-expression of serpin 8 gene resulted in a significant increase in fungal virulence. This study highlights that functional secretory signal sequences are potential molecular elements useful in excretion of virulence-related proteins in insect pathogenic fungi.

Identification of Laccase Family of Auricularia auricula-judae and Structural Prediction Using Alphafold.

Laccase is an enzyme that plays an important role in fungi, including lignin degradation, stress defense, and formation of fruiting bodies. Auricularia auricula-judae is a white-rot fungus in the Basidiomycota phylum, capable of delignifying wood. In this study, seven genes belonging to the laccase family were identified through de novo sequencing, containing Cu-Oxidase, Cu-Oxidase_2, and Cu-Oxidase_3 domains. Subsequently, the physical characteristics, phylogenetic relationships, protein secondary structure, and tertiary structure of the laccase family (AaLac1-AaLac7) were analyzed. Prediction of N-glycosylation sites identified 2 to 10 sites in the laccase family, with AaLac7 having the highest number of sites at 10. Sequence alignment and analysis of the laccase family showed high consistency in signature sequences. Phylogenetic analysis confirmed the relationship among laccases within the family, with AaLac3-AaLac4 and AaLac5-AaLac6 being closely positioned on the tree, exhibiting high similarity in tertiary structure predictions. This study identified and analyzed laccase family genes in Auricularia auricula-judae using de novo sequencing, offering a simple method for identifying and analyzing the laccase family in organisms with unknown genetic information.

Dual-localization signals enhance mitochondrial targeted presentation of engineered proteins.

Effective delivery of engineered proteins into mitochondria is of great significance for developing efficient mitochondrial DNA editing tools and realizing accurate treatment of mitochondrial diseases. Here, the candidate genes, eGFP and Cas9, were engineered with different mitochondrial localization signal (MLS) sequences introduced at their up- or/and down-streams. The corresponding expression vectors for the engineered proteins were constructed respectively, and HEK293T cells were transfected with these vectors. The fluorescence colocalization and Western blotting assays were used to analyze the mitochondrial targeting presentation effect of different engineered proteins. The results demonstrated that the daul-MLS modification of the eGFP and Cas9 proteins significantly improved the efficiency of mitochondrial targeted presentation, compared with the engineered proteins with single MLS added. Hence, it is speculated that dual MLS strategy can enhance the mitochondrial targeting of engineered proteins, which lays a theoretical foundation for the future development of efficient mitochondrial DNA editing tools.

HTS and scRNA-seq revealed that the location and RSS quality of the mammalian TRBV and TRBJ genes impact biased rearrangement

The quality of Recombination signal sequences (RSSs), location, and genetics of mammalian V, D, and J genes synergistically affect the recombination frequency of genes; however, the specific regulatory mechanism and efficiency have not been elucidated. By taking advantage of single-cell RNA-sequencing (scRNA-seq) and high-throughput sequencing (HTS) to investigate V(D)J rearrangement characteristics in the CDR3 repertoire, we found that the distal and proximal V genes (or J genes) “to D” gene were involved in rearrangement significantly more frequently than the middle V genes (or J genes) in the TRB locus among various species, including Primates (human and rhesus monkey), Rodentia (BALB/c, C57BL/6, and Kunming mice), Artiodactyla (buffalo), and Chiroptera (Rhinolophus affinis). The RSS quality of the V and J genes affected their frequency in rearrangement to varying degrees, especially when the V-RSSs with recombination signal information content (RIC) score < -45 significantly reduced the recombination frequency of the V gene. The V and J genes that were “away from D” had the dual advantages of recombinant structural accessibility and relatively high-quality RSSs, which promoted their preferential utilization in rearrangement. The quality of J-RSSs formed during mammalian evolution was apparently greater than that of V-RSSs, and the D-J distance was obviously shorter than that of V-D, which may be one of the reasons for guaranteeing that the “D-to-J preceding V-to-DJ rule” occurred when rearranged. This study provides a novel perspective on the mechanism and efficiency of V-D-J rearrangement in the mammalian TRB locus, as well as the biased utilization characteristics and application of V and J genes in the initial CDR3 repertoire.

Pair formation in Enchenopa treehoppers (Hemiptera: Membracidae) involves complex male–female duetting, and three stages of female mate choice

Abstract We explore the complexity of the signal repertoire and sequences of behavioural interactions involved in pair formation in Enchenopa binotata treehoppers, which communicate via plant-borne vibrational signals, and whose pair formation involves prolonged male-female duetting interactions. We recorded these interactions using laser vibrometry and video assays. In males, we report two phases of signalling: a searching phase in which males use a basic repertoire to solicit engagement from females; and a more complex phase incorporating additional signal types and elements males used once engaged by females. In females, we report a novel three-stage process of selective cooperation with males, as well as a novel signal type that was necessary but not sufficient for copulation to occur. These three stages include active duetting with a male that was necessary for him to locate and mount females; the novel signal that females produce after continued mounted duetting that prompts the male to attempt genital coupling; and the female actively allowing coupling. We discuss implications of our observations for these insects’ cognitive abilities in terms of the memory and selective attention required to sustain signalling interactions and proceed along the decision-making stages of mate choice. Using attention to detail as an aid to discovery, we aim to promote research on how such animals express such capabilities.

Deletion of mitochondrial DNA methyltransferase 1 contributes the development of murine heart failure under pressure overloaded

Abstract Background Mitochondrial DNA (mitDNA) has similarities to bacterial DNA, which contains inflammatogenic unmethylated CpG motifs. We found that mitDNA that escapes from autophagy causes inflammatory response and heart failure under pressure overload. DNA methyltransferase 1 (DNMT1) maintains methylation patterns in somatic cells. Deletion of DNMT1 results in embryonic lethality in mice and mitotic catastrophe in cultured cells. Additional possible translational start sites (ATG1, ATG2) are located upstream of the commonly accepted nuclear DNMT1 translational start site (ATG3) and there is a conserved mitochondrial translocation signal sequence between ATG1 and ATG3. The role of mitochondrial DNMT1 in the development of heart failure remains to be elucidated. Purpose The purpose of this study is to examine the in vivo role of mitochondrial DNMT1 in the heart under pressure overload. Methods We generated HA-tagged DNMT1 constructs, 1) starting from ATG1 (termed as whole) 2) from ATG3 (nuclear) and 3) from ATG3 and mutated in the nuclear translocation sequence (mitochondrial) and transfected HEK293 cells with the constructs. Localization of HA-tagged proteins was assessed by immunocytochemistry. We also generated mitochondrial DNMT1-deficient mice by inserting mutations into the ATG1 and ATG2. The mice were subjected to pressure overload by means of transverse aortic constriction (TAC) to induce heart failure. Cardiac remodelling was assessed by echocardiography as well as histological analyses 4 weeks after operation. Results Whole, nuclear and mitochondrial DMNT1 translocated to both mitochondria and nuclei, only nucleus and only mitochondria, respectively. Mitochondrial DNMT1-deficient mice were born at Mendelian frequency and grew to adulthood. Those showed no cardiac phenotypes under baseline conditions. However, the mice exhibited severe systolic dysfunction, indicated by left ventricular fractional shortening, 2 weeks after surgery compared with control littermates (control littermates 47.9% versus Mitochondrial DNMT1-deficient mice 32.3%, p&amp;lt;0.05). Intermuscular cell infiltration was observed in TAC-operated mitochondrial DNMT1-deficient hearts. Conclusions Mitochondrial DNA methyltransferase 1 plays a protective role in failing hearts and mitDNA methylation might be a therapeutic target to treat patients with heart failure.

Discrete‐time full‐order sensorless control of high‐speed interior permanent magnet synchronous motor in electric vehicle traction system

AbstractA discrete‐time full‐order sensorless control strategy for high‐speed interior permanent magnet synchronous motor (IPMSM) used in electric vehicle (EV) traction system is designed in this paper. While most speed and position observer (SPO) methods are developed in the continuous‐time domain, the presence of a unit‐time‐delay block existed in feedback loop and discretisation of the algorithm can lead to performance degradation during digital implementation. In this work, speed and angle are observed using the discrete‐time four‐order IPMSM model. A quadrature phase‐locked loop model with compensation is introduced, and its stability condition is established for the first time. Furthermore, to address the potential for sudden speed changes in vehicle applications, the parameter range is further refined to keep the estimation error within a specified range. The sliding mode observer is discretised and its stability is analysed using discrete Lyapunov theory. Additionally, the time sequence of interactive signals between SPO and field‐oriented control is thoroughly examined to ensure accurate time cycle. Finally, the proposed control strategy is validated and demonstrated through bench tests and real EV (LS6 of IM Motors) tests with a 190 kW IPMSM, which can improve the accuracy by 0.3 radians at 8000 rpm compared to traditional methods, and achieve stable control at 15,000 rpm on the test bench and at 120 kph with the EV.

Meta-analysis of ecological and phylogenetic biomass maturity metrics

Although a wide variety of biomass sources have been subjected to 16S rRNA gene sequencing, ecological and phylogenetic signatures of maturity have not been identified quantitatively. In this meta-analysis we reanalyzed data from the only published study with publicly available 16S and temperature data (Zhou et al., 2018), and then applied the Zhou results to 705 samples from 13 additional studies. Using the Zhou data, we found that Faith’s alpha diversity index correlated inversely with compost temperature and positively with maturity. We also noted a dramatic shift in the ratios of Bacilliota to Acidobacteriota, Planctomycetota, and Pseudomonadota, as samples cooled below 44 °C (p < 0.001). A negative correlation between Bacillota and Pseudomonadota was also observed in all 705 samples that included compost, sugarcane mill mud, anerobic digestates, and vermicompost. Even in the absence of temperature data for the majority of samples, our meta-analysis shows that microbiomes of diverse residuals converged on similar communities that resemble those of soil, regardless of the starting material or residual management process. We propose that approximately < 0.4 log(Bacillota:Pseudomonadota) and > 43 Faith’s phylogenetic diversity indices are indicative of maturity of diverse biomass materials destined for land application.

A vaccine candidate based on baculovirus displaying chikungunya virus E1-E2 envelope confers protection against challenge in mice.

Chikungunya fever is a re-emerging mosquito-borne disease caused by the chikungunya virus (CHIKV) and produces acute arthritis that can progress to chronic disease with arthralgia. The first approved live-attenuated chikungunya vaccine has only recently become available for use in humans in the USA, but the access in endemic regions remains unmet. Here, we exploited the baculovirus display technology to develop a vectored vaccine candidate that exposes the CHIKV membrane proteins E1 and E2 on the baculovirus surface. Using recombinant baculovirus as vector vaccines has both productive and regulatory advantages: they are safe for handling and easy to produce in high titers and are non-pathogenic and non-replicative in mammals but have strong adjuvant properties by inducing humoral and cellular immune responses. CHIKV E1 and E2 envelope proteins with their own signal and transmembrane sequences were expressed on the surface of budded baculovirus virions. Immunization of C57BL/6 mice with non-adjuvanted recombinant baculovirus induced IgG antibodies against E2 with a predominant IgG2c subtype, neutralizing antibodies and a specific IFN-γ CD8+ T-cell response. Immunization with a second dose significantly boosted the antibody response, and mice immunized with two doses of the vaccine candidate were completely protected against challenge with CHIKV showing no detectable viremia or signs of disease. Altogether, baculovirus display of CHIKV envelope proteins served as an efficient vaccine platform against CHIKV.IMPORTANCEThe global spread of chikungunya virus (CHIKV) has disproportionately impacted the Americas that experienced a fourfold increase in 2023 in cases and deaths compared with the same period in 2022. The disease is characterized by acute fever and debilitating joint pain that can become chronic. Despite the socioeconomic burden related to the high morbidity rates of CHIKV infection, a vaccine for CHIKV is currently approved only in the USA. Vaccines are the most effective preventive measure against viral diseases, and advances in the development of different vaccine platforms such as nucleic acids and viral vectors have prompted the rapid deployment of vaccines to contain the COVID-19 pandemic. Here, we report the use of baculovirus display as a strategy for the design of a novel vaccine that provides sterilizing immunity in a mouse model of chikungunya disease. Our results encourage further research regarding the potential of baculovirus as platforms for human vaccine design.

Molecular characterization of a novel thioredoxin-related transmembrane protein gene AcTMX3 that plays important roles in antioxidant defence in Arma chinensis diapause.

Protein disulphide isomerase (PDI) possesses disulphide isomerase, oxidoreductase and molecular chaperone activities, and is involved in regulating various physiological processes. However, there are few studies on the function in insect diapause. In this study, we cloned one novel member PDI family (TMX3, thioredoxin-related transmembrane protein 3) in Arma chinensis. The AcTMX3 encodes 426 amino acids that contains a predicted N-terminal signal sequence, a thioredoxin-like domain with the CXXC active site and a potential transmembrane region, which are typical sequence features of TMX3. RT-qPCR results showed that AcTMX3 was mainly expressed in the head under non-diapause conditions, while AcTMX3 was highly expressed in the fat body (central metabolic organ) under diapause conditions. Moreover, temporal expression profile showed that compared with non-diapause conditions, diapause conditions significantly induced AcTMX3 expression, and the expression of AcTMX3 was enhanced at 15°C. Silencing AcTMX3 in A. chinensis significantly inhibited the expression of antioxidant genes (AcTrx2 and AcTrx-like), increased the content of H2O2 and ascorbate and reduced the survival rate of A. chinensis under diapause conditions. Our results suggested that AcTMX3 played an important role in the resistance of A. chinensis to oxidative stress under diapause conditions.

Cross-sectional analysis of timber boards using convolutional long short-term memory neural networks

This paper proposes a one-dimensional convolutional long short-term memory (1D-CNN-LSTM) model for estimating the pith position and average ring width in Norway spruce timber boards. The model predicts these cross-sectional parameters by processing sequences of light-intensity signals derived from optical scans of the board’s four surfaces. The dataset used for training the model consists of synthetic boards sawn from simulated 3D logs. The model was evaluated on a dataset consisting of 552 end cross-sections from actual Norway spruce boards. Comparisons between the automatic and manual pith and ring width estimations demonstrated a very good accuracy. The computational speed of the model was more than twice as fast as the quickest method available in the literature. A large set of boards was then used to determine the advantages of incorporating the automatically determined average ring width in formulating indicating properties for machine strength grading. This evaluation revealed that the average ring width could, in certain situations, compensate for unknown variables such as density or resonance frequency in predicting the tensile and bending strength of Norway spruce boards.

CD4 T cells restricted to DRB1*15:01 recognize two Epstein–Barr virus glycoproteins capable of intracellular antigen presentation

Both genetic and environmental factors contribute to multiple sclerosis (MS) risk. Infection with the Epstein-Barr virus (EBV) is the strongest environmental risk factor, and HLA-DR15 is the strongest genetic risk factor for MS. We employed computational methods and in vitro assays for CD4 T cell activation to investigate the DR15-restricted response to EBV. Using a machine learning-based HLA ligand predictor, the EBV glycoprotein B (gB) was predicted to be enriched in epitopes restricted to presentation by DRB1*15:01. In DR15-positive individuals, two epitopes comprised the major CD4 T cell response to gB. Surprisingly, the expression of recombinant gB in a DR15-homozygous B cell line or primary autologous B cells elicited a CD4 T cell response, indicating that intracellular gB was loaded onto HLA class II molecules. By deleting the signal sequence of gB, we determined that this pathway for direct activation of CD4 T cells was dependent on trafficking to the endoplasmic reticulum (ER) within the B cell. We screened seven recombinant EBV antigens from the ER compartment for immune responses in DR15-negative vs. DR15-homozygous individuals. In addition to gB, gH was a key CD4 T cell target in individuals homozygous for DR15. Compared to non-DR15 controls, DR15-homozygotes had significantly higher T cell responses to both gB and gH but not to EBV latent or lytic antigens overall. Responses to gB and gH were slightly elevated in DR15 homozygotes with MS. Our results link MS environmental and genetic risk factors by demonstrating that HLA-DR15 dictates CD4 T cell immunity to EBV antigens.

Structural and functional insights from the sequences and complex domain architecture of adhesin-like proteins from Methanobrevibacter smithii and Methanosphaera stadtmanae.

Methanogenic archaea, or methanogens, are crucial in guts and rumens, consuming hydrogen, carbon dioxide, and other fermentation products. While their molecular interactions with other microorganisms are not fully understood, genomic sequences provide information. The first genome sequences of human gut methanogens, Methanosphaera stadtmanae and Methanobrevibacter smithii, revealed genes encoding adhesin-like proteins (ALPs). These proteins were also found in other gut and rumen methanogens, but their characteristics and functions remain largely unknown. This study analyzes the ALP repertoire of M. stadtmanae and M. smithii using AI-guided protein structure predictions of unique ALP domains. Both genomes encode more than 40 ALPs each, comprising over 10% of their genomes. ALPs contain repetitive sequences, many of which are unmatched in protein domain databases. We present unique sequence signatures of conserved ABD repeats in ALPs and propose a classification based on domain architecture. Our study offers insights into ALP features and how methanogens may interact with other microorganisms.

New Plasmid Constructs for Production of Yeast Based Oral Vaccines

In order to avoid conventional vaccines, there is an urgent need to look for new ways of vaccine generation that can cut down the cost, time, and the need for special requirements during storage and distribution. The development of oral peptide/protein-based vaccines could be an ideal alternative. Five expression plasmids are designed in this work for the production of Saccharomyces cerevisiae-based oral vaccines. Therefore, in this work genetic cassette with different organizations of the required genetic components for efficient gene expression is constructed in the pYES2 plasmid. The construction of five new plasmids for surface display of heterologous recombinant proteins in S. cerevisiae would enable easy insertion of the gene of interest into an optimized genetic cassette consisting of a strong host promoter GAL1, HA-tag for detection of recombinant enzymes, GAS1 gene with/without binding sequence coded for GAS1 cell wall protein and signal sequence for directing the protein into the secretory pathway. After the construction of the genetic cassettes, E gene coded for envelope protein of Chikungunya and Dengue virus is inserted in the genetic cassettes. Genetic models pYES2HAGAS1EgeneChikungunya, pYES2HAGAS1 Egene Dengue, pYES2GAS1 Egene ChikungunyaHA, and pYES2GAS1EGeneDengueHA are constructed with different genetic organizations to display envelope protein of Chikungunya and Dengue virus in the cell surface of S. cerevisiae. In the pYES2SignalEGeneDengueHA construction, envelope protein will be secreted by S. cerevisiae into the media. The constructed vectors are specialized to regulate the expression and surface display of heterologous recombinant proteins in Saccharomyces cerevisiae and will be suitable for large-scale oral vaccine production.

Proteome-scale structural prediction of the giant Marseillevirus reveals conserved folds and putative homologs of the hypothetical proteins.

A significant proportion of the highly divergent and novel proteins of giant viruses are termed "hypothetical" due to the absence of detectable homologous sequences in the existing databases. The quality of genome and proteome annotations often relies on the identification of signature sequences and motifs in order to assign putative functions to the gene products. These annotations serve as the first set of information for researchers to develop workable hypotheses for further experimental research. The structure-function relationship of proteins suggests that proteins with similar functions may also exhibit similar folding patterns. Here, we report the first proteome-wide structure prediction of the giant Marseillevirus. We use AlphaFold-predicted structures and their comparative analysis with the experimental structures in the PDB database to preliminarily annotate the viral proteins. Our work highlights the conservation of structural folds in proteins with highly divergent sequences and reveals potentially paralogous relationships among them. We also provide evidence for gene duplication and fusion as contributing factors to giant viral genome expansion and evolution. With the easily accessible AlphaFold and other advanced bioinformatics tools for high-confidence de novo structure prediction, we propose a combined sequence and predicted-structure-based proteome annotation approach for the initial characterization of novel and complex organisms or viruses.