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The quality of Beauveria bassiana conidia directly affects the virulence against insects. In this study, continuous subculturing of B. bassiana on both rice grains and potato dextrose agar (PDA) resulted in 55 and 49 % conidial yield reduction after 12 passages and 68 and 60 % virulence reduction after 20 and 12 passages at four d post-inoculation, respectively. The passage through Tenebrio molitor and Spodoptera exigua restored the virulence of rice and PDA subcultures, respectively. To explore the molecular mechanisms underlying the conidial quality and the decline of virulence after multiple subculturing, we investigated the conidial proteomic changes. Successive subculturing markedly increased the protein levels in oxidative stress response, autophagy, amino acid homeostasis, and apoptosis, but decreased the protein levels in DNA repair, ribosome biogenesis, energy metabolism, and virulence. The nitro blue tetrazolium assay verified that the late subculture's colony and conidia had a higher oxidative stress level than the early subculture. A 2A-type protein phosphatase and a Pleckstrin homology domain protein Slm1, effector proteins of the target of rapamycin (TOR) complex 1 and 2, respectively, were dramatically increased in the late subculture. These results suggest that TOR signalling might be associated with ageing in B. bassiana late subculture, in turn affecting its physiological characteristics and virulence.

Additional file 11. Fatty acid analysis profile obtained by using gas chromatography of Synechocystis sp. PCC6803 WT and Δsll0474 mutant.

Additional file 6. PPI subnetwork of Hik28. The subnetwork was constructed by using STRING. The A. platensis C1 proteins were inferred to that of the A. platensis NIES39 via orthologous group.

Additional file 2. PPI subnetworks of four groups of the differentially expressed proteins; (A) proteins upregulated at 22 °C and downregulated at 40 °C, (B) proteins downregulated at 22 °C and upregulated at 40 °C, (C) proteins upregulated at both temperatures (D) proteins downregulated at both temperatures. The subnetworks were constructed by using STRING. The A. platensis C1 proteins were inferred to that of the A. platensis NIES39 via orthologous group.

Additional file 8. PPI subnetwork of the bi-level regulated proteins. The subnetwork was constructed by using STRING. The A. platensis C1 proteins were inferred to that of the A. platensis NIES39 via orthologous group.

Additional file 7. PPI subnetwork of Hik28 and enzymes involved in fatty acid desaturation. The subnetwork was constructed by using STRING. The A. platensis C1 proteins were inferred to that of the Synechocystis sp. PCC6803 via orthologous group.

Additional file 5. Protein sequence alignment of the eukaryotic type Ser/Thr kinase, PkA, and the Ser/Thr kinases of A. platensis C1; (A) SPLC1_S240280, SPLC1_S032990 and SPLC1_S280030, and (B) SPLC1_S200190, SPLC1_S208550, SPLC1_S532860, SPLC1_S580170 and SPLC1_S541370. The conserved protein domains are labeled.

Background Bioactive peptides, including biological sources-derived peptides with different biological activities, are protein fragments that influence the functions or conditions of organisms, in particular humans and animals. Conventional methods of identifying bioactive peptides are time-consuming and costly. To quicken the processes, several bioinformatics tools are recently used to facilitate screening of the potential peptides prior their activity assessment in vitro and/or in vivo. In this study, we developed an efficient computational method, SpirPep, which offers many advantages over the currently available tools. Results The SpirPep web application tool is a one-stop analysis and visualization facility to assist bioactive peptide discovery. The tool is equipped with 15 customized enzymes and 1–3 miscleavage options, which allows in silico digestion of protein sequences encoded by protein-coding genes from single, multiple, or genome-wide scaling, and then directly classifies the peptides by bioactivity using an in-house database that contains bioactive peptides collected from 13 public databases. With this tool, the resulting peptides are categorized by each selected enzyme, and shown in a tabular format where the peptide sequences can be tracked back to their original proteins. The developed tool and webpages are coded in PHP and HTML with CSS/JavaScript. Moreover, the tool allows protein-peptide alignment visualization by Generic Genome Browser (GBrowse) to display the region and details of the proteins and peptides within each parameter, while considering digestion design for the desirable bioactivity. SpirPep is efficient; it takes less than 20 min to digest 3000 proteins (751,860 amino acids) with 15 enzymes and three miscleavages for each enzyme, and only a few seconds for single enzyme digestion. Obviously, the tool identified more bioactive peptides than that of the benchmarked tool; an example of validated pentapeptide (FLPIL) from LC-MS/MS was demonstrated. The web and database server are available at http://spirpepapp.sbi.kmutt.ac.th. Conclusion SpirPep, a web-based bioactive peptide discovery application, is an in silico-based tool with an overview of the results. The platform is a one-stop analysis and visualization facility; and offers advantages over the currently available tools. This tool may be useful for further bioactivity analysis and the quantitative discovery of desirable peptides. Electronic supplementary material The online version of this article (10.1186/s12859-018-2143-0) contains supplementary material, which is available to authorized users.

In nature, several abiotic stresses occur simultaneously, leading to retarded growth and biochemical changes in microalgae, including the commercial cyanobacterium, Arthrospira platensis. To gain more understanding of stress response, we investigated the integrative effects of nitrogen depletion and high temperature stress on physiological changes of A. platensis C1. The results revealed that photosynthetic activities of the stressed cells were markedly reduced by more than a half in comparison to the non-stressed cells. Moreover, a reduction of biomass was observed within 24 h after prolonged exposure to combined stress of nitrogen depletion and high temperature. The total protein contents, including phycocyanin (PC), in the stressed cells, decreased rapidly within 8 h of incubation. This finding was concomitant with the increase in carbohydrate content. However, the accumulation of carbohydrates in the nitrogen depletion-treated cells was greater than that in the cells under the combined stress. Furthermore, the levels of polysaccharides increased only under long-term incubation under nitrogen depletion but not under the combined stress. In addition, the combination of nitrogen depletion and high temperature stress resulted in an increase in the proportion of linoleic acid but a decrease in γ-linolenic acid within 24 h. These results suggest that the response of A. platensis to the combined stress was different from the responses of cells to individual stress. The PC degradation, the increased carbohydrates, and the alteration in fatty acids profiles were required for physiological response to combined nitrogen depletion and high temperature stress of A. platensis C1.

Arthrospira (Spirulina) platensis is a well-known commercial cyanobacterium that is used as a food and in feed supplements. In this study, we examined the physiological changes and whole-genome expression in A. platensis C1 exposed to high temperature. We found that photosynthetic activity was significantly decreased after the temperature was shifted from 35°C to 42°C for 2 h. A reduction in biomass production and protein content, concomitant with the accumulation of carbohydrate content, was observed after prolonged exposure to high temperatures for 24 h. Moreover, the results of the expression profiling in response to high temperature at the designated time points (8 h) revealed two distinct phases of the responses. The first was the immediate response phase, in which the transcript levels of genes involved in different mechanisms, including genes for heat shock proteins; genes involved in signal transduction and carbon and nitrogen metabolism; and genes encoding inorganic ion transporters for magnesium, nitrite and nitrate, were either transiently induced or repressed by the high temperature. In the second phase, the long-term response phase, both the induction and repression of the expression of genes with important roles in translation and photosynthesis were observed. Taken together, the results of our physiological and transcriptional studies suggest that dynamic changes in the transcriptional profiles of these thermal-responsive genes might play a role in maintaining cell homeostasis under high temperatures, as reflected in the growth and biochemical composition, particularly the protein and carbohydrate content, of A. platensis C1.

Bioactive peptides from natural sources are utilized as food supplements for disease prevention and are increasingly becoming targets for drug discovery due to their specificity, efficacy and the absence of undesirable side effects, among others. Hence, the ‘SpirPep’ platform was developed to facilitate the in silico-based bioactive peptide discovery of these highly sought-after biomolecules from Spirulina(Arthrospira platensis) and to select the protease (thermolysin) used for in vitro digestion. Analysis of the predicted and experimentally-derived peptides suggested that they were mainly involved in ACE inhibition; thus, an ACEi assay was used to study the ACE inhibitory activity of five candidate peptides (SpirPep1-5), chosen from common peptides with multifunctional bioactivity and 100% bioactive peptide coverage, originating from phycobiliproteins. Results showed that SpirPep1 inhibited the activity of ACE with IC50 of 1.748 mM and was non-toxic to fibroblasts of African green monkey kidney and human dermal skin. The molecular docking and MD simulation analysis revealed SpirPep1 had significantly lower binding scores than others and showed greater specificity to ACE. The non-bonded interaction energy of SpirPep1 and ACE was −883 kJ/mol. The SpirPep1 indirectly bound to ACE via the ACE substrate binding sites residues (D121, E123, S516, and S517) found in natural ACE inhibitory peptides (angiotensin II and bradykinin potentiating peptides). In addition, two unreported substrate binding sites including R124 and S219 were found. These results indicate that ‘SpirPep’ platform could increase the success rate for natural bioactive peptide discovery.

Algae and cyanobacteria have been studied for their feasibility to use as a source for production of bioproduct(s) due to their ability to absorb greenhouse gas (carbon dioxide) and to be grown large-scale outdoor cultures. Spirulina is the only cyanobacterium that can be mass cultivated in outdoor ponds, thus it can be a model organism for biofactory. Genome-scale study is relevant for screening of bioproduct synthetic capability, whereas proteome-wide analyses for protein expression level and posttranslational modification lead to information required for understanding of cellular response and regulation under abiotic stress conditions that the cells encounter in outdoor mass cultivation system. Here, we present our current understanding of protein networks in Spirulina, their regulation under temperature stress, and bioinformatics tools that are used for characterizing them. We then discuss the involvement of molecular chaperones, which play a vital role in protein quality control under stress conditions, in cellular protein networks.

Background Spirulina (Arthrospira) platensis is the only cyanobacterium that in addition to being studied at the molecular level and subjected to gene manipulation, can also be mass cultivated in outdoor ponds for commercial use as a food supplement. Thus, encountering environmental changes, including temperature stresses, is common during the mass production of Spirulina. The use of cyanobacteria as an experimental platform, especially for photosynthetic gene manipulation in plants and bacteria, is becoming increasingly important. Understanding the mechanisms and protein-protein interaction networks that underlie low- and high-temperature responses is relevant to Spirulina mass production. To accomplish this goal, high-throughput techniques such as OMICs analyses are used. Thus, large datasets must be collected, managed and subjected to information extraction. Therefore, databases including (i) proteomic analysis and protein-protein interaction (PPI) data and (ii) domain/motif visualization tools are required for potential use in temperature response models for plant chloroplasts and photosynthetic bacteria. Descriptions A web-based repository was developed including an embedded database, SpirPro, and tools for network visualization. Proteome data were analyzed integrated with protein-protein interactions and/or metabolic pathways from KEGG. The repository provides various information, ranging from raw data (2D-gel images) to associated results, such as data from interaction and/or pathway analyses. This integration allows in silico analyses of protein-protein interactions affected at the metabolic level and, particularly, analyses of interactions between and within the affected metabolic pathways under temperature stresses for comparative proteomic analysis. The developed tool, which is coded in HTML with CSS/JavaScript and depicted in Scalable Vector Graphics (SVG), is designed for interactive analysis and exploration of the constructed network. SpirPro is publicly available on the web at http://spirpro.sbi.kmutt.ac.th. Conclusions SpirPro is an analysis platform containing an integrated proteome and PPI database that provides the most comprehensive data on this cyanobacterium at the systematic level. As an integrated database, SpirPro can be applied in various analyses, such as temperature stress response networking analysis in cyanobacterial models and interacting domain-domain analysis between proteins of interest.

Iron is an essential element for life. However, the iron overload can be toxic. Here, we investigated the significant increase of tenellin and iron-tenellin complex production in ferricrocin-deficient mutants of Beauveria bassiana. Our chemical analysis indicated that the ferricrocin-deficient mutants T1, T3 and T5 nearly abolished ferricrocin production. In turn, these mutants had significant accumulation of iron-tenellin complex in their mycelia at 247-289 mg g(-1) cell dry weight under iron-replete condition. Both tenellin and iron-tenellin complex were not detected in the wild-type under such condition. Mass analysis of the mutants' crude extracts demonstrated that tenellin formed a 3:1 complex with iron in the absence of ferricrocin. The unexpected link between ferricrocin and tenellin biosynthesis in ferricrocin-deficient mutants could be a survival strategy during iron-mediated oxidative stress.

The present study focused on comparative proteome analyses of low- and high-temperature stresses and potential protein-protein interaction networks, constructed by using a bioinformatics approach, in response to both stress conditions. The data revealed two important points: first, the results indicate that low-temperature stress is tightly linked with oxidative stress as well as photosynthesis; however, no specific mechanism is revealed in the case of the high-temperature stress response. Second, temperature stress was revealed to be linked with nitrogen and ammonia assimilation. Moreover, the data also highlighted the cross-talk of signaling pathways. Some of the detected signaling proteins, e.g., Hik14, Hik26 and Hik28, have potential interactions with differentially expressed proteins identified in both temperature stress conditions. Some differentially expressed proteins found in the Spirulina protein-protein interaction network were also examined for their physical interactions by a yeast two hybrid system (Y2H). The Y2H results obtained in this study suggests that the potential PPI network gives quite reliable potential interactions for Spirulina. Therefore, the bioinformatics approach employed in this study helps in the analysis of phenomena where proteome analyses of knockout mutants have not been carried out to directly examine for specificity or cross-talk of signaling components.

Arthrospira platensis is a cyanobacterium that is extensively cultivated outdoors on a large commercial scale for consumption as a food for humans and animals. It can be grown in monoculture under highly alkaline conditions, making it attractive for industrial production. Here we describe the complete genome sequence of A. platensis C1 strain and its annotation. The A. platensis C1 genome contains 6,089,210 bp including 6,108 protein-coding genes and 45 RNA genes, and no plasmids. The genome information has been used for further comparative analysis, particularly of metabolic pathways, photosynthetic efficiency and barriers to gene transfer.

The present study examined the changes in protein expression in Spirulina platensis upon exposure to high temperature, with the changes in expression analyzed at the subcellular level. In addition, the transcriptional expression level of some differentially expressed proteins, the expression pattern clustering, and the protein-protein interaction network were analyzed. The results obtained from differential expression analysis revealed up-regulation of proteins involved in two-component response systems, DNA damage and repair systems, molecular chaperones, known stress-related proteins, and proteins involved in other biological processes, such as capsule formation and unsaturated fatty acid biosynthesis. The clustering of all differentially expressed proteins in the three cellular compartments showed: (i) the majority of the proteins in all fractions were sustained tolerance proteins, suggesting the roles of these proteins in the tolerance to high temperature stress, (ii) the level of resistance proteins in the photosynthetic membrane was 2-fold higher than the level in two other fractions, correlating with the rapid inactivation of the photosynthetic system in response to high temperature. Subcellular communication among the three cellular compartments via protein-protein interactions was clearly shown by the PPI network analysis. Furthermore, this analysis also showed a connection between temperature stress and nitrogen and ammonia assimilation.