Protease Gene Research Articles

Analysis of Cathepsin-L and Cathepsin-B Gene Expression in Embryonated Eggs of Fasciola gigantica and Effect of Various Protease Inhibitors on Miracidial Hatching

Background: Fasciola gigantica is a helminth parasite of veterinary importance and a constraint on the growth and productivity of domestic livestock in the tropical countries of Asia and Africa. Present study aimed at determining the expression of four cysteine protease genes including cathepsin (cat) L-1 D and cat-Bs in the embryonated egg stage of F. gigantica by polymerase chain reaction (PCR). In addition to the analysis of expression of the above genes in the embryonated eggs, inhibition of in vitro hatching of the miracidia from the eggs was carried out using three protease inhibitors viz. serine, cysteine and leucine aminopeptidase inhibitors to understand the possible role of these proteases in the hatching of the miracidia from the eggs. Methods: Cat- L-1D, cat B-1, cat B-2 and cat B-3 genes were amplified by reverse transcriptase and quantitative-PCR, respectively for determining their expression in the embryonated eggs. Inhibition of in vitro hatching of the miracidia from the eggs was carried out by exposing the embryonated eggs to different concentrations of iodoacetamide, phenyl methyl sulphonyl fluoride and bestatin as cysteine, serine and leucine aminopeptidase inhibitors. Result: Results showed that cat L1-D, cat B-1 and cat B-3 genes were expressed at the embryonated egg stage but cat B-2 gene was not expressed at this stage of the parasite. Iodoacetamide and phenyl methyl sulphonyl fluoride (cysteine and serine protease inhibitors) inhibited the miracidial hatching at different concentrations, indicating probable role of cysteine and serine proteases in its hatching process. However, leucine aminopeptoidase does not seem to influence the miracidial hatching from the eggs as bestatin did not inhibit its hatching.

Transcriptome analysis of different life-history stages and screening of male-biased genes in Daphnia sinensis

BackgroundIn the life history of Daphnia, the reproductive mode of parthenogenesis and sexual reproduction alternate in aquatic ecosystem, which are often affected by environmental and genetic factors. Recently, the sex-biased genes are of great significance for clarifying the origin and evolution of reproductive transformation and the molecular regulation mechanism of sex determination in Daphnia. Although some genes on reproductive transition of Daphnia had been researched, molecular mechanism on the maintenance of sexually dimorphic phenotypes of Daphnia are still not well known, including differentially expressed genes in different life-history stages.ResultsIn this study, four life-history stages of Daphnia sinensis, juvenile female (JF), parthenogenetic female (PF), sexual female (SF) and male (M), were performed for transcriptome, and male-biased genes were screened. A total of 110437 transcripts were obtained and assembled into 22996 unigenes. In the four life-history stages (JF, PF, SF and M), the number of unique unigenes is respectively 2863, 445, 437 and 586, and the number of common unigenes is 9708. The differentially expressed genes (DEGs) between male and other three female stages (M vs JF, M vs PF and M vs SF) were 4570, 4358 and 2855, respectively. GO gene enrichment analysis showed that the up-regulated genes in male were mainly enriched in hydrolase activity and peptidase activity. Thirty-six genes in male were significantly higher expression than in the three female stages, including one Doublesex (Dsx) gene, one laminin gene, five trypsin genes and one serine protease genes, and one chitin synthase gene and two chitinase genes.ConclusionsOur results showed that thirty-six candidate genes may be as the male-biased genes involving in the maintenance of sexually dimorphic phenotypes. This work will provide a reference for further exploring the functional genes related to sex differentiation in Daphnia species. Moreover, according to previous investigations, we thought that the expression level of functional genes may be related to the life-history stages of organisms, and may be also affected by different Daphnia species.

Next-generation sequencing (NGS) reveals low-abundance HIV-1 drug resistance mutations among patients experiencing virological failure at the time of therapy switching in Uganda

Background: The emergence and spread of antiretroviral drug resistant HIV-1 variants is one of the major factors associated with therapeutic failure in persons living with HIV (PLWH) as it jeopardizes the efforts to reduce the progression to AIDS. Whereas Sanger sequencing is the most appropriate conventional method for HIV drug resistance testing, it has limited capacity to detect low-abundance variants. This study assessed the suitability of next generation sequencing (NGS) to reveal low-abundance HIV-1 drug resistance mutations amongst patients experiencing virological failure at the time of therapy switching in Uganda. Methods: Archived blood samples previously collected from 60 PLWH were used in this study. Briefly HIV viral RNA was extracted and performed targeted NGS of portions of both the HIV protease and reverse transcriptase genes on the illumina MiSeq. For performance comparison, Sanger sequencing was also performed for all the samples targeting the highlighted genes. The sequence data generated was analyzed using HyDRA bioinformatics pipeline, accompanied by the Stanford HIV drug resistance database, to annotate and report drug resistance mutations/variants. Results: Out of the 60 samples, 58 passed preliminary quality control and were considered for subsequent analysis—of which 38/58 (65.5%) registered low-abundance HIV drug resistance variants. Overall, 757 variants from the NGS data and 90 variants from the Sanger data were identified. The most prevalent minority variants included; K65R (65.5%), K14R (63.8%), K45R (63.8%), L63P (63.8%), I15V (63.8%), K70R (60.3%), V77I (60.3%), L283I (60.3%), G16E (58.6%) and L282C (58.6%). Conclusion: An estimated 65.5% of the sampled population harbors low-abundance HIV-1 variants, most of which are associated with virological failure, and consequently antiviral drug resistance. NGS suitably detects drug resistance mutations even at frequencies below 20% of the viral quasi species that are occasionally missed by Sanger sequencing.

Co‐occurrences of soil nitrogen cycling and human‐disease genes following spent mushroom substrate and nitrification inhibitor applications: A strategy for decreasing health risk

AbstractSpent mushroom substrates can be utilized as organic fertilizer in agricultural production but may pose a health risk. Nitrification inhibitors dicyandiamide and 3,4‐dimethylpyrazole phosphate have been used to enhance fertilizer nitrogen utilization efficiency. However, the changes of soil abiotic properties, microbial activities, nitrogen cycling and human‐disease genes, and their comprehensive relationships after the spent mushroom substrate and nitrification inhibitor applications were still unknown. In this study, the spent mushroom substrate and nitrification inhibitor were applied into the agricultural soils at the rates of 2.5% (w/w) and 1.0% of nitrogen content in the spent mushroom substrate, respectively, and then lettuce was planted. Compared with the control, spent mushroom substrate application significantly increased the lettuce biomass, soil enzyme activities and chitinase, protease, nitric‐oxide reductase, nitrogenase, and urease gene abundances. However, the antibiotic resistance and human‐disease gene abundances were also significantly enhanced following the spent mushroom substrate application. Relative to spent mushroom substrate alone, the dicyandiamide application significantly decreased the soil pH and human‐disease gene abundances, although extra dicyandiamide and 3,4‐dimethylpyrazole phosphate enhanced 61.4% and 45.0% of dry biomass of aboveground lettuce. The human‐disease gene abundances were positively correlated with soil pH but were negatively correlated with the Acidobacteria and Streptomyces ratios in soils. Spent mushroom substrate application could generate double‐edged sword effects, and the health risk should be considered in the spent mushroom substrate applications. Extra dicyandiamide application could further promote crop growth while decrease the human‐disease risk from the spent mushroom substrate.

HtrA1L364P leads to cognitive dysfunction and vascular destruction through TGF‐β/Smad signaling pathway in CARASIL model mice

AimsCerebral autosomal recessive arteriopathy with subcortical infarcts and leukoencephalopathy (CARASIL) is a life‐threatening, inherited, nonhypertensive arteriole disease of the brain. Therapeutic strategy for CARASIL is limited because its pathogenesis is not clear. We previously reported the first family with CARASIL in China, which involves a high‐temperature requirement serine protease gene mutation (HtrA1L364P). Based on this previous study, we constructed a CARASIL mouse model (Mut‐hHtrA1L364P mouse, hereinafter referred to as Mut). This paper aimed to systematically study the behavior, pathology, and molecular biology of Mut mice and explore the pathogenesis and possible therapeutic strategies of CARASIL.MethodsFood maze and water maze experiments were used in the behavioral studies. Pathological studies were carried out by arteriole labeling staining and electron microscopy. The mRNA and protein expression levels of the key factors of TGF‐β/Smad signaling pathway (TGF‐β, Smad2, Smad3, and Smad4) in the brain of the model mice were detected by immunohistochemistry, real‐time quantitative polymerase chain reaction (RT‐PCR), and Western blot assay.ResultsThe food maze and water maze experiment data showed significant differences between the Mut and wild‐type (WT) mice in the first time to find food, the time to contact the escape table for the first time, and the number of times to travel in the escape table quadrant (p < 0.001). The results of vascular labeling staining showed that some small arteries in the brain of Mut mice lost normal structure. The results of electron microscopy showed that the cell morphologies in the cortex and hippocampus of Mut mice were abnormal; the number of synapses was reduced; the walls of capillaries, venules, and arterioles thickened; lumen stenosis and other abnormal phenomenon occurred; and lipofuscin deposition and autophagosomes were found in the hippocampus. Immunohistochemistry, RT‐PCR, and Western Blot results showed that the mRNA and protein expression levels of TGF‐β, Smad2, and Smad3 in the brain of Mut mice increased to different degrees.ConclusionsThe most significant innovation of this study is the first study on the pathogenesis of CARASIL disease using model animals. The Mut mice can well simulate the pathogenesis of CARASIL in behavioral and pathological aspects. The TGF‐β/Smad signaling pathway, which is involved in the pathogenesis of CARASIL, is abnormally upregulated in the brain of Mut mice.

Genome-wide identification and expression analysis of the ftsH protein family and its response to abiotic stress in Nicotiana tabacum L

BackgroundThe filamentous temperature-sensitive H protease (ftsH) gene family plays an important role in plant growth and development. FtsH proteins belong to the AAA protease family. Studies have shown that it is a key gene for plant chloroplast development and photosynthesis regulation. In addition, the ftsH gene is also involved in plant response to stress. At present, the research and analysis of the ftsH gene family are conducted in microorganisms such as Escherichia coli and Oenococcus and various plants such as Arabidopsis, pear, rice, and corn. However, analysis reports on ftsH genes from tobacco (Nicotiana tabacum L.), an important model plant, are still lacking. Since ftsH genes regulate plant growth and development, it has become necessary to systematically study this gene in an economically important plant like tobacco.ResultsThis is the first study to analyze the ftsH gene from Nicotiana tabacum L. K326 (NtftsH). We identified 20 ftsH genes from the whole genome sequence, renamed them according to their chromosomal locations, and divided them into eight subfamilies. These 20 NtftsH genes were unevenly distributed across the 24 chromosomes. We found four pairs of fragment duplications. We further investigated the collinearity between these genes and related genes in five other species. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis identified differential expression patterns of NtftsH in different tissues and under various abiotic stress conditions.ConclusionsThis study provides a comprehensive analysis of the NtftsH gene family. The exon–intron structure and motif composition are highly similar in NtftsH genes that belong to the same evolutionary tree branch. Homology analysis and phylogenetic comparison of ftsH genes from several different plants provide valuable clues for studying the evolutionary characteristics of NtftsH genes. The NtftsH genes play important roles in plant growth and development, revealed by their expression levels in different tissues as well as under different stress conditions. Gene expression and phylogenetic analyses will provide the basis for the functional analysis of NtftsH genes. These results provide a valuable resource for a better understanding of the biological role of the ftsH genes in the tobacco plant.

Biogeographic Variation and Functional Pathways of the Gut Microbiota in Celiac Disease

Genes and gluten are necessary but insufficient to cause celiac disease (CeD). Altered gut microbiota has been implicated as an additional risk factor. Variability in sampling site may confound interpretation and mechanistic insight, as CeD primarily affects the small intestine. Thus, we characterized CeD microbiota along the duodenum and in feces and verified functional impact in gnotobiotic mice. We used 16S rRNA gene sequencing (Illumina) and predicted gene function (PICRUSt2) in duodenal biopsies (D1, D2 and D3), aspirates, and stool from patients with active CeD and controls. CeD alleles were determined in consented participants. A subset of duodenal samples stratified according to similar CeD risk genotypes (controls DQ2-/- or DQ2+/- and CeD DQ2+/-) were used for further analysis and to colonize germ-free mice for gluten metabolism studies. Microbiota composition and predicted function in CeD was largely determined by intestinal location. In the duodenum, but not stool, there was higher abundance of Escherichia coli (D1), Prevotella salivae (D2), and Neisseria (D3) in CeD vs controls. Predicted bacterial protease and peptidase genes were altered in CeD and impaired gluten degradation was detected only in mice colonized with CeD microbiota. Our results showed luminal and mucosal microbial niches along the gut in CeD. We identified novel microbial proteolytic pathways involved in gluten detoxification that are impaired in CeD but not in controls carrying DQ2, suggesting an association with active duodenal inflammation. Sampling site should be considered a confounding factor in microbiome studies in CeD.

Biochemical characterization of a novel oxidatively stable, halotolerant, and high-alkaline subtilisin from Alkalihalobacillus okhensis Kh10-101T.

Halophilic and halotolerant microorganisms represent a promising source of salt‐tolerant enzymes suitable for various biotechnological applications where high salt concentrations would otherwise limit enzymatic activity. Considering the current growing enzyme market and the need for more efficient and new biocatalysts, the present study aimed at the characterization of a high‐alkaline subtilisin from Alkalihalobacillus okhensis Kh10‐101T. The protease gene was cloned and expressed in Bacillus subtilis DB104. The recombinant protease SPAO with 269 amino acids belongs to the subfamily of high‐alkaline subtilisins. The biochemical characteristics of purified SPAO were analyzed in comparison with subtilisin Carlsberg, Savinase, and BPN'. SPAO, a monomer with a molecular mass of 27.1 kDa, was active over a wide range of pH 6.0–12.0 and temperature 20–80 °C, optimally at pH 9.0–9.5 and 55 °C. The protease is highly oxidatively stable to hydrogen peroxide and retained 58% of residual activity when incubated at 10 °C with 5% (v/v) H2O2 for 1 h while stimulated at 1% (v/v) H2O2. Furthermore, SPAO was very stable and active at NaCl concentrations up to 5.0 m. This study demonstrates the potential of SPAO for biotechnological applications in the future.

Conjugational Transformation of Wild Type Bacillus halodurans CM1 by Methylated Recombinant Plasmid Harbouring a Gene Encoding for Alkaline Protease and the Protease Activity Assay of the Transformant

Protease contributes significantly to various industrial sectors, as shown by its increasing demand. An indigenous previously isolated bacteria, Bacillus halodurans CM1, is a wild-type bacterium whose ability to produce alkalotermophilic protease. In this study, the transformation of methylated pBBRE194 plasmid containing alkaline protease gene from this strain (PBBRE194-prot-CM1) into itself using a conjugation approach was conducted, and the measurement of the alkaline protease activity of the recombinant bacterium was carried out. The recombinant B. halodurans CM1 has been verified to carry the methylated pBBRE194 prot-CM1 by examining its ability to degrade protein in media containing skim milk and tetracycline, but also by amplifying tetracycline resistance gene sequence with 1,024 bp length of plasmid pBBRE194 prot-CM1 by PCR method from the recombinant bacterium. The results confirmed that recombinant B. halodurans CM1 was positively harboring plasmid pBBRE194 prot-CM1. Alkaline protease produced by recombinant CM1 reached higher activity than wild type between 18-36 h of cultivation. The alkalotermophilic wild type B. halodurans could accept the recombinant plasmid into their cells via conjugational transformation is firstly reported to our further knowledge.

De novo transcriptome sequencing and functional annotation of Demodex canis.

Demodex canis is an important parasitic mite causing skin lesions in dogs. However, molecular studies on this species are limited because of the lack of transcriptomic data. To obtain functional genes of D. canis, mites were collected and RNA was extracted for transcriptome sequencing and functional annotation. Coding sequences (CDSs) of important functional genes were screened and identified using bioinformatics strategies. Six complete CDSs were amplified by specific primers, cloned and sequenced. Results demonstrated that the quantity of the RNA extracted from 100 mites was 12.8ng and the RNA integrity number was 5.4, indicating that it could be used to construct a cDNA library. Transcriptome sequencing yielded 263,619 unigenes, of which 151,048 (57.3%) were functionally annotated. Using bioinformatics strategies, 58 total CDSs were identified as homologous to those of closely related mite species, including 16 types of allergen genes, 13 types of protease genes, and nine types of motion-related genes. The verified CDSs were almost identical to the CDSs of unigenes. Phylogenetic analyses of tropomyosin further revealed that the verified CDSs clustered successively with those of Demodex species and Tetranychus species in Raphignathae, which agreed with the morphological classification, demonstrating the reliability of the transcriptomic data. In conclusion, this study is the first to successfully sequence transcriptome of D. canis, perform functional annotation, and verify CDSs, which will provide ample data for further studies on the functional genes and molecular pathogenic mechanism of D. canis.

Biochemical Characterisation and Structure Determination of a Novel Cold-Active Proline Iminopeptidase from the Psychrophilic Yeast, Glaciozyma antarctica PI12

Microbial proteases constitute one of the most important groups of industrially relevant enzymes. Proline iminopeptidases (PIPs) that specifically release amino-terminal proline from peptides are of major interest for applications in food biotechnology. Proline iminopeptidase has been extensively characterised in bacteria and filamentous fungi. However, no similar reports exist for yeasts. In this study, a protease gene from Glaciozyma antarctica designated as GaPIP was cloned and overexpressed in Escherichia coli. Sequence analyses of the gene revealed a 960 bp open reading frame encoding a 319 amino acid protein (35,406 Da). The purified recombinant GaPIP showed a specific activity of 3561 Umg−1 towards L-proline-p-nitroanilide, confirming its identity as a proline iminopeptidase. GaPIP is a cold-active enzyme with an optimum activity of 30 °C at pH 7.0. The enzyme is stable between pH 7.0 and 8.0 and able to retain its activity at 10–30 °C. Although GaPIP is a serine protease, only 25% inhibition by the serine protease inhibitor, phenylmethanesulfonylfluoride (PMSF) was recorded. This enzyme is strongly inhibited by the presence of EDTA, suggesting that it is a metalloenzyme. The dimeric structure of GaPIP was determined at a resolution of 2.4 Å. To date, GaPIP is the first characterised PIP from yeasts and the structure of GaPIP is the first structure for PIP from eukaryotes.

A risk variant for Barrett's esophagus and esophageal adenocarcinoma at chr8p23.1 affects enhancer activity and implicates multiple gene targets.

Nineteen genetic susceptibility loci for esophageal adenocarcinoma (EAC) and its precursor Barrett's esophagus (BE) have been identified through genome-wide association studies (GWAS). Clinical translation of such discoveries, however, has been hindered by the slow pace of discovery of functional/causal variants and gene targets at these loci. We previously developed a systematic informatics pipeline to prioritize candidate functional variants using functional potential scores, applied the pipeline to select high-scoring BE/EAC risk loci and validated a functional variant at chr19p13.11 (rs10423674). Here, we selected two additional prioritized loci for experimental interrogation: chr3p13/rs1522552 and chr8p23.1/rs55896564. Candidate enhancer regions encompassing these variants were evaluated using luciferase reporter assays in two EAC cell lines. One of the two regions tested exhibited allele-specific enhancer activity - 8p23.1/rs55896564. CRISPR-mediated deletion of the putative enhancer in EAC cell lines correlated with reduced expression of three candidate gene targets: B lymphocyte kinase (BLK), nei like DNA glycosylase 2 (NEIL2) and cathepsin B (CTSB). Expression quantitative trait locus (eQTL) mapping in normal esophagus and stomach revealed strong associations between the BE/EAC risk allele at rs55896564 (G) and lower expression of CTSB, a protease gene implicated in epithelial wound repair. These results further support the utility of functional potential scores for GWAS variant prioritization, and provide the first experimental evidence of a functional variant and risk enhancer at the 8p23.1 GWAS locus. Identification of CTSB, BLK and NEIL2 as candidate gene targets suggests that altered expression of these genes may underlie the genetic risk association at 8p23.1 with BE/EAC.

Genome-Wide Comprehensive Survey of the Subtilisin-Like Proteases Gene Family Associated With Rice Caryopsis Development.

Subtilisin-like proteases (SUBs), which are extensively distributed in three life domains, affect all aspects of the plant life cycle, from embryogenesis and organogenesis to senescence. To explore the role of SUBs in rice caryopsis development, we recharacterized the OsSUB gene family in rice (Oryza sativa ssp. japonica). In addition, investigation of the SUBs was conducted across cultivated and wild rice in seven other Oryza diploid species (O. brachyantha, O. glaberrima, O. meridionalis, O. nivara, O. punctata, O. rufipogon, and O. sativa ssp. indica). Sixty-two OsSUBs were identified in the latest O. sativa ssp. japonica genome, which was higher than that observed in wild species. The SUB gene family was classified into six evolutionary branches, and SUB1 and SUB3 possessed all tandem duplication (TD) genes. All paralogous SUBs in eight Oryza plants underwent significant purifying selection. The expansion of SUBs in cultivated rice was primarily associated with the occurrence of tandem duplication events and purifying selection and may be the result of rice domestication. Combining the expression patterns of OsSUBs in different rice tissues and qRT–PCR verification, four OsSUBs were expressed in rice caryopses. Moreover, OsSUBs expressed in rice caryopses possessed an earlier origin in Oryza, and the gene cluster formed by OsSUBs together with the surrounding gene blocks may be responsible for the specific expression of OsSUBs in caryopses. All the above insights were inseparable from the continuous evolution and domestication of Oryza. Together, our findings not only contribute to the understanding of the evolution of SUBs in cultivated and wild rice but also lay the molecular foundation of caryopsis development and engineering improvement of crop yield.

Peptidase Regulation in Trichophyton rubrum Is Mediated by the Synergism Between Alternative Splicing and StuA-Dependent Transcriptional Mechanisms.

Trichophyton rubrum is the most common causative agent of dermatophytosis worldwide and uses keratinized substrates such as skin and nails as its main source of nutrition during infection. Its pathogenic character relies on colonization and viability maintenance at the target host sites. Since fungal physiology must adapt and respond to host conditions for the successful establishment of infection, biological mechanisms are constantly being triggered by T. rubrum to guarantee its survival in the host environment. The ability of this fungus to sense and modulate the secretion of specific proteases according to environmental pH signaling is considered as a pivotal virulence factor for effective invasion and persistence of infection in the host. Transcriptional regulation of genes encoding specific proteases, such as peptidases, is a key biological process that drives physiological modulation to meet fungal requirements. It accomplishes a robust balance among transcript isoforms that can be directed to perform distinct cellular functions. Thus, alternative splicing mechanisms are suitable for fungal cells to establish a balance toward reprogramming protein translation to impair or boost physiological conditions. In this study, we investigated the role of alternative splicing, especially intron retention events, in generating isoforms of virulence factors in T. rubrum mediated by transcriptional coordination of the protein StuA, a recently described transcription factor in this fungus. By analyzing the previous gene expression data provided by RNA-sequencing and after validation by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR), we observed that two peptidase-coding genes (TERG_00734 and TERG_04614) could be direct targets of alternative splicing in the presence of keratin. Furthermore, protease isoforms generated by alternative splicing in T. rubrum were also detected in a co-culture with human keratinocytes, highlighting the role of these proteins in keratin deconstruction. Our results strongly suggest the influence of StuA on the regulation of virulence factors in T. rubrum and dermatophyte infections by triggering the transcription of the peptidase genes mentioned above in an alternative splicing-independent balance. The results elucidate how fungal cells drive alternate splicing to promote physiological adaptations and show that transcriptional regulation and virulence traits are robust elements required for dermatophyte infection.

Detection of Virulence-Associated Genes and in vitro Gene Transfer From Aeromonas sp. Isolated From Aquatic Environments of Sub-himalayan West Bengal.

Aeromonas is omnipresent in aquatic environments and cause disease within a wide host range. A total of thirty-four isolates from water samples of small fish farms were identified as Aeromonas based on biochemical characteristics and 16S rRNA gene sequence. A total of six virulent factors were analyzed which indicated 100% of isolates as beta-haemolytic and proteolytic, whereas 44.1, 38.2, and 70.6% of isolates produced DNAse, siderophore, and amylase, respectively. Studies on the occurrence of four genetic determinants of virulence factors revealed that aer/haem (haemolytic toxin) and flaA (polar flagella) genes were present in 44.1% of strains whereas ascV (type 3 secretion system) and aspA (serine protease) genes were detected in 21.5 and 8.82% of strains, respectively. Fish (Anabas testudineus) challenge studies showed that the isolate GP3 (Aeromonas veronii) bearing five virulent factors with the combination of aer/haem+/ascV+/fla+ genes induced severe lesions leading to 100% of mortality. In contrast, RB7 possessing four virulence factors and three genes (aer/haem+/ascV+/aspA+) could not produce severe lesions and any mortality indicating the absence of correlation between the virulence factors, its genes, and the pathogenicity in fishes. GP3 was cytotoxic to human liver cell line (WRL-68) in trypan blue dye exclusion assay. The 431 bp aer/haem gene of GP3 was transferable to E. coli Dh5α with a conjugational efficiency of 0.394 × 10–4 transconjugants per recipient cell. The transfer was confirmed by PCR and by the presence of 23-kb plasmids in both donor and transconjugants. Therefore, the occurrence of mobile genetic elements bearing virulence-associated genes in Aeromonas indicates the need for periodic monitoring of the aquatic habitat to prevent disease outbreaks.

Efficient production of extracellular alkaline protease in Bacillus amyloliquefaciens by host strain construction

Bacillus amyloliquefaciens is an important industrial microorganism, which can be applied as a protein expression host. However, the extracellular protein expression ability of B. amyloliquefaciens is still low. Hence, it is necessary to develop a B. amyloliquefaciens host with a high extracellular protein expression capacity. In this study, B. amyloliquefaciens HZ-12 was the original strain, then seven important extracellular protease genes (epr, nprE, aprE-a, mpr, pbpF, vpr, ykct1), one important intracellular protease gene (aprX) and two redundant proteins genes (htrB, hag) were deleted in HZ-12, resulting in B. amyloliquefaciens BAX-10. In order to evaluate the extracellular protein expression ability of BAX-10, the alkaline protease gene aprE from Bacillus subtilis D7 was expressed in BAX-10. After fermentation, the alkaline protease activity of BAX-10/aprE reached 666.82 U/mL, which was 57% higher than that of the control strain HZ/aprE. Moreover, the deletion of the ten genes had no negative effect on the growth of B. amyloliquefaciens. In summary, B. amyloliquefaciens BAX-10 could be used as a potential platform host for expression of target extracellular proteins.

Analysis of virological response to therapy and resistance profile in treatment-experienced and naive HIV-1 infected Romanian patients receiving regimens containing darunavir boosted with ritonavir or cobicistat.

77% of Romanians infected with HIV receive antiretroviral therapy, with the challenge of maintaining long-term therapeutic success (the viral load becoming/remaining undetectable). The main purpose of this study was to provide comparative analysis of the long-term virological response to therapeutic regimens containing pharmacokinetically enhanced darunavir (DRV) with ritonavir (RTV) or cobicistat (COBI). The second aim was to evaluate the viral resistance profile to therapy, by number/type/frequency of viral mutations. This retrospective study was conducted on 462 patients infected with subtype F HIV-1, registered at the "Matei Bals" National Institute of Infectious Diseases, between 2018 and 2021: 384 patients received (among other ARV) DRV 600mg, enhanced with RTV 100mg (twice daily) and 78 patients received DRV 800mg boosted with COBI 150mg (once daily). The virological response was measured by determining the viral load (HIV-1 RNA copies/mL), while the incidence of viral resistance to therapy was assessed by genotyping tests. Comparing the patients with undetectable viremia, from the 1st visit to the 3rd one, the outcomes showed that at the last visit, 84.6% subjects in the DRV/c group achieved virological efficiency over those from DRV/r group (76.8%). The differences observed between this time points are statistically significant p<0.05. DRV/c administered in combination with other ARV, in subtype F HIV-1 infected patients, proved to be more virologically effective, maintaining a favorable long-time result. When comparing the outcomes of the two groups, a statistically significant difference of p<0.05 was obtained. 32 patients (27 from DRV/r group and 5 from DRV/c group) were evaluated with persistent HIV-1 ARN plasma load >1000 copies/mL, during all 3 clinical visits. They formed a research sub-group evaluated in terms of resistance to therapy and were reported as virological failures. 28.12% of the sub-group with persistent HIV-1 RNA >1000 copies/mL were from the DRV/r group and only 3.12% from the DRV/c group. Drug mutations (DRM) involved in antiretroviral resistance/sensitivity occurred both in the protease gene, and in the reverse transcriptase gene, with the involved ARV classes being protease inhibitors, nucleoside reverse transcriptase inhibitors, non-nucleoside reverse transcriptase inhibitors. 16 different types of mutations were evaluated in the PR gene and 20 mutations were evaluated in RT gene.

Determination of the efficacy of using a serine protease gene as a DNA vaccine to protect against Vibrio parahaemolyticus infection in Litopenaeus vannamei

Serine proteases are proteolytic enzymes that exhibit biological roles in many biological systems. Previously, a Vibrio parahaemolyticus serine protease was reported to be a virulence factor. Here, the serine protease gene of V. parahaemolyticus was investigated as a DNA vaccine against V. parahaemolyticus in Litopenaeus vannamei. The serine protease gene was mutated to replace the conserved residues His82, Asp131 and Ser231 with Gly, Asp and Pro, respectively. Then, a pcDNA3.1 vector to express mutVpSP (mutant serine protease) was constructed for in vitro and in vivo DNA vaccine investigation. In vivo mutVpSP transcriptional analysis revealed expression in various immunized white shrimp tissues, such as hemocytes, hepatopancreas, stomach, intestine, gills, and muscle. The efficiency of prevention of V. parahaemolyticus infection was investigated in vaccinated shrimp, and the lowest cumulative mortality percentage was 30%, while the control shrimp had a 60% cumulative mortality rate. The immune system was stimulated in shrimp vaccinated with the DNA vaccine. The mRNA expression of the shrimp immune-responsive genes phenoloxidase, peroxinectin and C-type lectin was significantly upregulated. Additionally, the humoral and cellular immune responses, including the PO, phagocytic, and encapsulation activities and nodule formation, were elevated. These results suggested that the serine protease could be a V. parahaemolyticus virulence determinant and that this DNA vaccine could be applied as an effective vaccine candidate for control of acute hepatopancreatic necrosis disease syndrome (AHPND) in shrimp.

Competence shut-off by intracellular pheromone degradation in salivarius streptococci.

Competence for DNA transformation is a major strategy for bacterial adaptation and survival. Yet, this successful tactic is energy-consuming, shifts dramatically the metabolism, and transitory impairs the regular cell-cycle. In streptococci, complex regulatory pathways control competence deactivation to narrow its development to a sharp window of time, a process known as competence shut-off. Although characterized in streptococci whose competence is activated by the ComCDE signaling pathway, it remains unclear for those controlled by the ComRS system. In this work, we investigate competence shut-off in the major human gut commensal Streptococcus salivarius. Using a deterministic mathematical model of the ComRS system, we predicted a negative player under the control of the central regulator ComX as involved in ComS/XIP pheromone degradation through a negative feedback loop. The individual inactivation of peptidase genes belonging to the ComX regulon allowed the identification of PepF as an essential oligoendopeptidase in S. salivarius. By combining conditional mutants, transcriptional analyses, and biochemical characterization of pheromone degradation, we validated the reciprocal role of PepF and XIP in ComRS shut-off. Notably, engineering cleavage site residues generated ultra-resistant peptides producing high and long-lasting competence activation. Altogether, this study reveals a proteolytic shut-off mechanism of competence in the salivarius group and suggests that this mechanism could be shared by other ComRS-containing streptococci.

The First Homologous Expression System for the β-Lytic Protease of Lysobacter capsici VKM B-2533T, a Promising Antimicrobial Agent.

A successful homologous expression system based on Lysobacter capsici VKM B-2533T and the plasmid pBBR1-MCS5 was first developed for a promising bacteriolytic enzyme of this bacterium, β-lytic protease (Blp). In the expression strains, blp gene expression under the regulation of the GroEL(A) and T5 promoters increased by 247- and 667-fold, respectively, as compared with the wild-type strain. After the cultivation of the expression strains L. capsici PGroEL(A)-blp and L. capsici PT5-blp, the Blp yield increased by 6.7- and 8.5-fold, respectively, with respect to the wild-type strain. The cultivation of the expression strain L. capsici PT5-blp was successfully scaled up. Under fermentation conditions the yield of the enzyme increased by 1.6-fold. The developed homologous system was used to express the gene of the bacteriolytic serine protease (Serp) of L. capsici VKM B-2533T. The expression of the serp gene in L. capsici PT5-serp increased by 585-fold. The developed homologous system for the gene expression of bacteriolytic Lysobacter enzymes is potentially biotechnologically valuable, and is promising for creating highly efficient expression strains.