Genome-wide characterization and expression analysis of the HD-Zip II gene family in response to drought and GA3 stresses in Nicotiana tabacum.

BACKGROUND: Homeodomain-leucine ZIPper (HD-ZIP) transcription factors play crucial roles in plant growth, development, and stress responses. The HD-ZIP family is categorised into four groups (HD-ZIP I-IV). While extensive genome-wide studies have been conducted on the HD-ZIP I, III, and IV subfamily in Nicotiana tabacum (tobacco), comprehensive reports on the HD-ZIP II subfamily genes are limited. METHODS: Bioinformatics resources and tools were utilised to analyse molecular characteristics, phylogenetic homology, and protein interactions. Expression pattern analyses in various tissues and the relative expression of NtHD-ZIP II genes under drought and GA3 treatment were assessed by qRT-PCR. RESULTS: In this study, 24 HD-ZIP II members were systematically identified and categorised into seven independent clades through phylogenetic analysis involving tobacco and other plant species. We found that 19 NtHD-ZIP II genes exhibited tissue-specific expression. The transcripts of NtHD-ZIPII3, 4, 14, 23, 24 were notably induced under the drought treatments, while those of NtHD-ZIPII7, 11, 12, 20 were suppressed. Furthermore, NtHD-ZIPII15 transcripts decreased following GA3 treatment, whereas the transcripts of NtHD-ZIPII7, 8, 11, 12 were induced after GA3 treatment. Notably, an increase in trichomes was observed in tobacco leaves treated with GA3 and subjected to drought. CONCLUSIONS: The expression levels of some HD-ZIP II genes were altered, and an increase in glandular trichomes was induced under GA3 and drought treatments in tobacco. Overall, our findings provide insights into the expression patterns of NtHD-ZIP II genes and will facilitate their functional characterisation in future studies.

Key candidate genes for male sterility in peppers unveiled via transcriptomic and proteomic analyses.

This study aimed to enhance the use of male sterility in pepper to select superior hybrid generations. Transcriptomic and proteomic analyses of fertile line 1933A and nucleic male sterility line 1933B of Capsicum annuum L. were performed to identify male sterility-related proteins and genes. The phylogenetic tree, physical and chemical characteristics, gene structure characteristics, collinearity and expression characteristics of candidate genes were analyzed. The study identified 2,357 differentially expressed genes, of which 1,145 and 229 were enriched in the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases, respectively. A total of 7,628 quantifiable proteins were identified and 29 important proteins and genes were identified. It is worth noting that the existence of CaPRX genes has been found in both proteomics and transcriptomics, and 3 CaPRX genes have been identified through association analysis. A total of 66 CaPRX genes have been identified at the genome level, which are divided into 13 subfamilies, all containing typical CaPRX gene conformal domains. It is unevenly distributed across 12 chromosomes (including the virtual chromosome Chr00). Salt stress and co-expression analysis show that male sterility genes are expressed to varying degrees, and multiple transcription factors are co-expressed with CaPRXs, suggesting that they are involved in the induction of pepper salt stress. The study findings provide a theoretical foundation for genetic breeding by identifying genes, metabolic pathways, and molecular mechanisms involved in male sterility in pepper.

Morphological and phylogenetic characterisation of two new soil-borne fungal taxa belonging to Clavicipitaceae (Hypocreales, Ascomycota).

The fungal taxa belonging to the Clavicipitaceae (Hypocreales, Ascomycota) are widely distributed and include diverse saprophytic, symbiotic and pathogenic species that are associated with soils, insects, plants, fungi and invertebrates. In this study, we identified two new fungal taxa belonging to the family Clavicipitaceae that were isolated from soils collected in China. Morphological characterisation and phylogenetic analyses showed that the two species belong to Pochonia (Pochoniasinensissp. nov.) and a new genus for which we propose Paraneoaraneomycesgen. nov. in Clavicipitaceae.

Biocontrol Capabilities of Bacillus subtilis E11 against Aspergillus flavus In Vitro and for Dried Red Chili (Capsicum annuum L.).

As a condiment with extensive nutritional value, chili is easy to be contaminated by Aspergillus flavus (A. flavus) during field, transportation, and storage. This study aimed to solve the contamination of dried red chili caused by A. flavus by inhibiting the growth of A. flavus and detoxifying aflatoxin B1 (AFB1). In this study, Bacillus subtilis E11 (B. subtilis) screened from 63 candidate antagonistic bacteria exhibited the strongest antifungal ability, which could not only inhibit 64.27% of A. flavus but could also remove 81.34% of AFB1 at 24 h. Notably, scanning electron microscopy (SEM) showed that B. subtilis E11 cells could resist a higher concentration of AFB1, and the fermentation supernatant of B. subtilis E11 could deform the mycelia of A. flavus. After 10 days of coculture with B. subtilis E11 on dried red chili inoculated with A. flavus, the mycelia of A. flavus were almost completely inhibited, and the yield of AFB1 was significantly reduced. Our study first concentrated on the use of B. subtilis as a biocontrol agent for dried red chili, which could not only enrich the resources of microbial strains for controlling A. flavus but also could provide theoretical guidance to prolong the shelf life of dried red chili.

Acremoniumcapsici and A.guizhouense, two new members of Acremonium (Hypocreales, Sordariomycetes) isolated from the rhizosphere soil of Capsicumannuum.

Two new species, Acremoniumcapsici and A.guizhouense, isolated from the rhizosphere soil of Capsicumannuum, are described and illustrated. Two-locus DNA sequences based on phylogeny, in combination with the morphology of the asexual morph, were used to characterize these species. In the phylogenetic tree, both new species clustered into a monophyletic clade with strong support, distinct from other previously known species of Acremonium. The new species differed from their allied species in their morphology.

rocF affects the production of tetramethylpyrazine in fermented soybeans with Bacillus subtilis BJ3-2.

BACKGROUND: Tetramethylpyrazine (TTMP) is a flavoring additive that significantly contributes to the formation of flavor compounds in soybean-based fermented foods. Over recent years, the application of TTMP in the food industry and medicine has been widely investigated. In addition, several methods for the industrial-scale production of TTMP, including chemical and biological synthesis, have been proposed. However, there have been few reports on the synthesis of TTMP through amino acid metabolic flux. In this study, we investigated genetic alterations of arginine metabolic flux in solid-state fermentation (SSF) of soybeans with Bacillus subtilis (B.subtilis) BJ3-2 to enhance the TTMP yield. RESULTS: SSF of soybeans with BJ3-2 exhibited a strong Chi-flavour (a special flavour of ammonia-containing smelly distinct from natto) at 37 °C and a prominent soy sauce-like aroma at 45 °C. Transcriptome sequencing and RT-qPCR verification showed that the rocF gene was highly expressed at 45 °C but not at 37 °C. Moreover, the fermented soybeans with BJ3-2ΔrocF (a rocF knockout strain in B. subtilis BJ3-2 were obtained by homologous recombination) at 45 °C for 72 h displayed a lighter color and a slightly decreased pH, while exhibiting a higher arginine content (increased by 14%) than that of BJ3-2. However, the ammonia content of fermented soybeans with BJ3-2ΔrocF was 43% lower than that of BJ3-2. Inversely, the NH4+ content in fermented soybeans with BJ3-2ΔrocF was increased by 28% (0.410 mg/kg). Notably, the TTMP content in fermented soybeans with BJ3-2ΔrocF and BJ3-2ΔrocF + Arg (treated with 0.05% arginine) were significantly increased by 8.6% (0.4617 mg/g) and 18.58% (0.504 mg/g) respectively than that of the BJ3-2. CONCLUSION: The present study provides valuable information for understanding the underlying mechanism during the TTMP formation process through arginine metabolic flux.

Multi-omics analyses of the mechanism for the formation of soy sauce-like and soybean flavor in Bacillus subtilis BJ3-2.

Although soy sauce-like flavor and soybean flavor are two key contributors to the flavor of fermented foods, the key compounds of soy sauce-like flavor and soybean flavor and production mechanisms are still poorly understood and need further investigation. In the present study, we found that the Bacillus subtilis (B. subtilis) BJ3-2 strain has various metabolic properties at different temperatures, and the strain cultured at 37℃ increased the soybean flavor (a special flavor of ammonia-containing smelly distinct from natto) compared with culturing at 45℃ and 53℃. Interestingly, the strain cultured at 45℃ and 53℃ had a higher soy sauce-like flavor than that in 37℃. Moreover, a comparative transcriptome analysis of the strain cultured at 37℃, 45℃, and 53℃ showed transcriptional changes related to secondary metabolites and ABC transporters, which is critical for the amino acid transport and metabolism in B. subtilis. Meanwhile, proteomics and metabolomics profiling showed a marked change in amino acids transport and metabolism. In addition, the metabolic analysis revealed a significant metabolic difference (including sulfur metabolism, glutathione metabolism, nicotinate and nicotinamide metabolism, cysteine and methionine metabolism, and pyrimidine metabolism) in the strain cultured at 45℃ and 53℃ compared to 37℃. To sum, this study used the multi-omics profiling tool to investigate the fermentative strains B. subtilis BJ3-2, thus providing a deeper insight into the mechanism of the formation of soy sauce-like flavor and soybean flavor compounds.