Penicillium Arizonense as a Novel Producer Strain for Mycophenolic Acid and Expression Analysis of Biosynthesizing Gene Clusters

A novel potent mycophenolic acid (MPA) producer strain of the genus Penicillium was isolated from refrigerated Mozzarella cheese and identified as P. arizonenseHEWt1. The molecular mechanism of MPA production by this new isolate was our main target. To achieve this objective, we first isolated three MPA overproducer mutants by exposing the wild type to different doses of gamma-rays, and the fermentation conditions for the highest production of MPA by both the wild type and mutants were optimized. Then, orthologs of MPA gene clusters in P. brevicompactum were cloned and predicted from the genome of P. arizonense. Sequencing and bioinformatic analysis proved the presence of a cluster containing five putative genes in the P. arizonense HEWt1 genome ortholog to the MPA cluster, mpaA, mpaC, mpaF, mpaG, and mpaH. All predicted genes displayed 96-97% similarity with the related hypothetical protein of P. arizonense. The genes, mpaG, mpaC, and mpaF. represented 69%, 82%, 84%, respectively, similarity with their orthologous genes in P. brevicompactum, whereas mpaG and mpaA represented 75% and 79%, respectively, similarity to their orthologous genes in P. roqueforti. Gene expression analysis through quantitative rPCR indicated an increase in the transcription value of all annotated genes in the three mutants over the wild type. A highly significant increase in the gene expression of mpaC, mpaF, and mpaH was observed, with 8.4561±1.02, 5.6569±0.87, and 4.6268±0.18-fold increases, respectively, in P. arizonense-MT1 compared with wild-type. These results confirmed the potential participation of these genes in MPA biosynthesis and are the first report regarding the molecular mechanism of MPA production by P. arizonense.

Simple Bayesian Gene Network Learning in Populus Drought Transcriptome Data

Constructing a sensibly functional gene interaction network is highly appealing for better understanding system-level biological processes governing various Populus traits. Bayesian Network (BN) learning provides an elegant and compact statistical approach for modeling causal gene-gene relationships in microarray data. Therefore, it could come with the illumination of functional molecular playing in Biology Systems. In the present study, different forms of gene Bayesian networks were detected on Populus cellular transcriptome data. Markov blankets would likely be emerging at every possible gene regulatory Bayesian network level. Results showed that PtpAffx.1257.4.S1_a_at,1.0 hypothetical protein is the most important in its possible regulatory program. This paper illustrates that the gene network regulatory inference is possible to encapsulate within a single BN model. Therefore, such a BN model can serve as a promising training tool for Populus gene expression data for better future experimental scenarios. Bangladesh J. Bot. 50(4): 1077-1086, 2021 (December)

In-silico characterization and structure-based functional annotation of a hypothetical protein from Campylobacter jejuni involved in propionate catabolism

Campylobacter jejuni is one of the most prevalent organisms associated with foodborne illness across the globe causing campylobacteriosis and gastritis. Many proteins of C. jejuni are still unidentified. The purpose of this study was to determine the structure and function of a non-annotated hypothetical protein (HP) from C. jejuni. A number of properties like physiochemical characteristics, 3D structure, and functional annotation of the HP (accession No. CAG2129885.1) were predicted using various bioinformatics tools followed by further validation and quality assessment. Moreover, the protein-protein interactions and active site were obtained from the STRING and CASTp server, respectively. The hypothesized protein possesses various characteristics including an acidic pH, thermal stability, water solubility, and cytoplasmic distribution. While alpha-helix and random coil structures are the most prominent structural components of this protein, most of it is formed of helices and coils. Along with expected quality, the 3D model has been found to be novel. This study has identified the potential role of the HP in 2-methylcitric acid cycle and propionate catabolism. Furthermore, protein-protein interactions revealed several significant functional partners. The in-silico characterization of this protein will assist to understand its molecular mechanism of action better. The methodology of this study would also serve as the basis for additional research into proteomic and genomic data for functional potential identification.

Plasmodium berghei-Released Factor, PbTIP, Modulates the Host Innate Immune Responses

The Plasmodium parasite has to cross various immunological barriers for successful infection. Parasites have evolved mechanisms to evade host immune responses, which hugely contributes to the successful infection and transmission by parasites. One way in which a parasite evades immune surveillance is by expressing molecular mimics of the host molecules in order to manipulate the host responses. In this study, we report a Plasmodium berghei hypothetical protein, PbTIP (PbANKA_124360.0), which is a Plasmodium homolog of the human T-cell immunomodulatory protein (TIP). The latter possesses immunomodulatory activities and suppressed the host immune responses in a mouse acute graft-versus-host disease (GvHD) model. The Plasmodium berghei protein, PbTIP, is expressed on the merozoite surface and exported to the host erythrocyte surface upon infection. It is shed in the blood circulation by the activity of an uncharacterized membrane protease(s). The shed PbTIP could be detected in the host serum during infection. Our results demonstrate that the shed PbTIP exhibits binding on the surface of macrophages and reduces their inflammatory cytokine response while upregulating the anti-inflammatory cytokines such as TGF-β and IL-10. Such manipulated immune responses are observed in the later stage of malaria infection. PbTIP induced Th2-type gene transcript changes in macrophages, hinting toward its potential to regulate the host immune responses against the parasite. Therefore, this study highlights the role of a Plasmodium-released protein, PbTIP, in immune evasion using macrophages, which may represent the critical strategy of the parasite to successfully survive and thrive in its host. This study also indicates the human malaria parasite TIP as a potential diagnostic molecule that could be exploited in lateral flow-based immunochromatographic tests for malaria disease diagnosis.

Enzyme systems involved in glucosinolate metabolism in Companilactobacillus farciminis KB1089

Cruciferous vegetables are rich sources of glucosinolates (GSLs). GSLs are degraded into isothiocyanates, which are potent anticarcinogens, by human gut bacteria. However, the mechanisms and enzymes involved in gut bacteria-mediated GSL metabolism are currently unclear. This study aimed to elucidate the enzymes involved in GSL metabolism in lactic acid bacteria, a type of gut bacteria. Companilactobacillus farciminis KB1089 was selected as a lactic acid bacteria strain model that metabolizes sinigrin, which is a GSL, into allylisothiocyanate. The sinigrin-metabolizing activity of this strain is induced under glucose-absent and sinigrin-present conditions. A quantitative comparative proteomic analysis was conducted and a total of 20 proteins that were specifically expressed in the induced cells were identified. Three candidate proteins, β-glucoside-specific IIB, IIC, IIA phosphotransferase system (PTS) components (CfPttS), 6-phospho-β-glucosidase (CfPbgS) and a hypothetical protein (CfNukS), were suspected to be involved in sinigrin-metabolism and were thus investigated further. We hypothesize a pathway for sinigrin degradation, wherein sinigrin is taken up and phosphorylated by CfPttS, and subsequently, the phosphorylated entity is degraded by CfPbgS. As expression of both pttS and pbgS genes clearly gave Escherichia coli host strain sinigrin converting activity, these genes were suggested to be responsible for sinigrin degradation. Furthermore, heterologous expression analysis using Lactococcus lactis suggested that CfPttS was important for sinigrin degradation and CfPbgS degraded phosphorylated sinigrin.

Apple gene MD13G1109800 is a member of Trihelix family transcription factors and expressed in response to abiotic stress

The Trihelix family of transcription factors plays an important role in the plant’s response to various abiotic stress types. In this work in apple Golden Delicious genome we identified apple gene MD13G1109800 as a member of Triheilx family in silico. Analysis of chromosomal localization showed that it is located on chromosome 13 and has four introns. The hypothetical protein encoded by it has a length of 365 amino acid residues, a molecular weight of 42097.23 Da, an isoelectric point pI = 6.21 and located in the nucleus. Analysis of the promoter region of the MD13G1109800 gene indicates that its product is a member of many signaling pathways triggered by both external and internal factors. The expression level of the MD13G1109800 gene increases under drought, low and high temperatures, as well as salinity in the MM-106 apple rootstock.

Role of the Filifactor alocis Hypothetical Protein FA519 in Oxidative Stress Resistance

Filifactor alocis is an emerging member of the periodontal community and is now proposed to be a diagnostic indicator of periodontal disease. However, due to the lack of genetic tools available to study this organism, not much is known about its virulence attributes.

Virtual Screening to Identify the Protein Network Interaction of Triclosan in Red Complex Pathogens

Background: Antimicrobial drug resistance is the major problem encountered world-wide. Novel therapeutic leads have been identified and are regularly tested for their activity against microbial pathogens. Aim: To identify the protein network interactions of triclosan in red complex pathogens. Materials and Methods: The present study follows an observational study design which aims to screen for the interaction of triclosan in red complex pathogens. The interaction was analyzed using the STITCH v.5 pipeline. The functional class of proteins identified were assessed using VICMPred and VirulentPred softwares. The microbial pathogens Treponema denticola ATCC 35405, Tannerella forsythia ATCC 43037, Porphyromonas gingivalis ATCC 33277 are the strains of red complex pathogens that are included in the present study. Results and Discussion: Several proteins were found to interact with triclosan. Among the protein interactions, interactions of triclosan with virulent proteins seems to have a greater impact. The NAD-dependent nucleotide-diphosphate-sugar epimerase [PGN_1370], Putative NAD dependent epimerase [PGN_1886], GDP-fucose synthetase [PGN_1079], Probable oxidoreductase [PGN_1360] of Porphyromonas gingivalis, Conserved hypothetical protein [TDE_2401], Epimerase/dehydratase family protein [TDE_1439] of Treponema denticola, NAD dependent epimerase/dehydratase family protein [BFO_2919], Hypothetical protein [BFO_1782], Nitroreductase family protein [BFO_1604] and Nitroreductase family protein [BFO_1516] Tannerella forsythia were found to be exhibit virulence nature. Conclusion: This study identifies the molecular targets of triclosan on red complex pathogens. As triclosan interacts with the red complex pathogens, in future it can be used as a primary medicine for periodontitis and some oral conditions.

A previously unrecognized membrane protein in the Rhodobacter sphaeroides LH1-RC photocomplex

Rhodobacter (Rba.) sphaeroides is the most widely used model organism in bacterial photosynthesis. The light-harvesting-reaction center (LH1-RC) core complex of this purple phototroph is characterized by the co-existence of monomeric and dimeric forms, the presence of the protein PufX, and approximately two carotenoids per LH1 αβ-polypeptides. Despite many efforts, structures of the Rba. sphaeroides LH1-RC have not been obtained at high resolutions. Here we report a cryo-EM structure of the monomeric LH1-RC from Rba. sphaeroides strain IL106 at 2.9 Å resolution. The LH1 complex forms a C-shaped structure composed of 14 αβ-polypeptides around the RC with a large ring opening. From the cryo-EM density map, a previously unrecognized integral membrane protein, referred to as protein-U, was identified. Protein-U has a U-shaped conformation near the LH1-ring opening and was annotated as a hypothetical protein in the Rba. sphaeroides genome. Deletion of protein-U resulted in a mutant strain that expressed a much-reduced amount of the dimeric LH1-RC, indicating an important role for protein-U in dimerization of the LH1-RC complex. PufX was located opposite protein-U on the LH1-ring opening, and both its position and conformation differed from that of previous reports of dimeric LH1-RC structures obtained at low-resolution. Twenty-six molecules of the carotenoid spheroidene arranged in two distinct configurations were resolved in the Rba. sphaeroides LH1 and were positioned within the complex to block its channels. Our findings offer an exciting new view of the core photocomplex of Rba. sphaeroides and the connections between structure and function in bacterial photocomplexes in general.