Multi-omics Data Reveals the Impact of Sodium Butyrate on Gene Expression and Protein Modification in Streptomyces

Academic Background

Streptomyces has attracted widespread attention due to its rich gene clusters and potential for producing a large number of natural products. Histone deacetylase (HDAC) inhibitors play an important role in histone modification in fungi, but their role in prokaryotes is less known. Particularly in Streptomyces, whether these inhibitors can affect the biosynthesis of secondary metabolites remains a question worth studying. The development of modern bioinformatics has led to the discovery of a large number of antibiotic biosynthetic gene clusters (BGCs) in Streptomyces, but under laboratory culture conditions, most of these gene clusters are in a silent state and unable to express diverse bioactive products. Therefore, activating these silent BGCs is an important strategy for developing new bioactive compounds.

Paper Source

This study was written by a team of professors including Liu Shuangjiang and Tan Huarong from the Institute of Microbiology, Chinese Academy of Sciences, and was published in “Genomics Proteomics & Bioinformatics” on September 2, 2022. This article discusses the global impact of the HDAC inhibitor sodium butyrate (SB) on the synthesis of secondary metabolites in Streptomyces, especially its activating effect on silent BGCs.

Research Process

Experimental Subject

This study used Streptomyces olivaceus FXJ 8.021, isolated from marine sediments, as a model strain to investigate the effects of SB on the biosynthesis of secondary metabolites. The complete genome sequencing of strain FXJ 8.021 showed that it contains a linear chromosome and a plasmid, with a GC content of 72.39%, encoding 7385 proteins, 18 rRNAs, 66 tRNAs, and 63 non-coding RNAs.

Experimental Steps

1. Prediction of BF content and gene analysis: The genome of strain FXJ 8.021 was analyzed using antiSMASH, predicting 33 secondary metabolite synthesis gene clusters. Among these clusters, 14 are related to the synthesis of various secondary metabolites, including polyketides and non-ribosomal peptides.
2. Effect of SB on the expression of silent BGCs: Through RT-PCR and HPLC analysis, it was determined that SB can activate the silent Lobophorin BGC, and the effects of other HDAC inhibitors (SAHA, VA) were also explored. The results showed that SB can significantly enhance the biosynthesis of Lobophorin.
3. Chemical structure analysis: The fermentation broth was extracted with ethyl acetate and analyzed by HPLC and NMR to determine the chemical structures of Lobophorin A and B.
4. Transcriptomics analysis: RNA-Seq results showed that in the presence of SB, 2471 genes in FXJ 8.021 were significantly affected in their expression levels, with 1333 genes upregulated and 1138 genes downregulated.

Novel Methods and Techniques

1. Multi-omics analysis: This study combined genomics, transcriptomics, and protein acetylation omics to elucidate the global cellular response of Streptomyces to SB.
2. Protein interaction network analysis: Through protein-protein interaction (PPI) networks, the complex hierarchical relationships of SB regulating gene expression and metabolite synthesis in Streptomyces were analyzed.

Main Research Findings

1. Gene cluster activation: RT-PCR analysis and antiSMASH prediction results were consistent, showing that SB activated the silent Lobophorin BGC, and RNA-Seq data confirmed the upregulation of Lobophorin biosynthesis genes.
2. Acetylomics analysis: LC-MS/MS analysis showed changes in protein acetylation in FXJ 8.021 after SB treatment, identifying 1473 acetylated proteins, with 218 acetylation sites upregulated and 411 acetylation sites downregulated.
3. Precursor molecule accumulation: After SB treatment, the intracellular concentrations of CoA ester precursors (such as acetyl-CoA and methylmalonyl-CoA) in FXJ 8.021 increased significantly, promoting the biosynthesis of Lobophorin.

Conclusion

This study reveals that the HDAC inhibitor SB activates secondary metabolite synthesis gene clusters by regulating the protein acetylation levels in Streptomyces and promoting the accumulation of metabolite precursors. This research not only provides an effective strategy for activating silent BGCs in Streptomyces but also deepens the understanding of protein acetylation regulation of primary and secondary metabolism in Streptomyces.

Research Significance and Application Value

1. Scientific value: The study reveals the global impact of SB on the synthesis of secondary metabolites in Streptomyces, providing an example of the application of bacterial HDAC inhibitors in microbial metabolic regulation.
2. Application value: By activating silent BGCs, this research provides potential methods for developing new antibiotics, helping to address public health challenges posed by antibiotic resistance and emerging pathogens.

Research Highlights

1. Newly discovered antibiotics: For the first time, it was confirmed that SB can activate the silent Lobophorin gene cluster in Streptomyces, revealing the potential regulatory mechanism of acetylation modification in bacteria.
2. Innovative technology: Comprehensive application of multi-omics analysis methods systematically revealed the complex cellular response of Streptomyces in the presence of SB.
3. Broad impact: By regulating the acetylation levels in Streptomyces, the study demonstrates the application potential of SB in improving the production of bioactive substances.

Other Valuable Information

The research team emphasized the in-depth analysis of SB treatment on protein acetylation and global acetylation changes. In the future, based on this research, they will further explore the application extension of these small molecule inhibitors in microbial metabolism regulation and utilization, especially in exploring the fine-tuned regulatory mechanisms of bacterial nucleoid-associated proteins (NAPs).