Biochemical and structural analyses reveal critical residues in δ subunit affecting its bindings to β′ subunit of Staphylococcus aureus RNA polymerase

Lin, Zhaozhu; Wang, Fulin; Shang, Zhuo; Lin, Wei

doi:10.1016/j.bbrc.2021.01.078

Cited by 6 publications

(4 citation statements)

References 21 publications

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“…26,27) The vital roles of RNAP are related to the pathogenicity, RNA polymerase function, and transcriptional integrity of SAU. [27][28][29] In the two-component system, several down regulated proteins, such as ptpA, D-alanyl carrier protein (dltC), and arlR_1, are potential antibiotic targets and play pivotal roles in regulating SAU virulence gene expression, cell wall synthesis, and biofilm formation. The two-component system protein ptpA interferes with host cell signaling 30,31) and contributes to the infectivity of SAU.…”

Section: Discussionmentioning

confidence: 99%

Proteomic Analysis of <i>Staphylococcus aureus</i> Treated with ShangKeHuangShui

Liu,

Zhao,

Yang

et al. 2024

Biological & Pharmaceutical Bulletin

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Staphylococcus aureus (SAU) stands as the prevailing pathogen in post-traumatic infections, with the emergence of antibiotic resistance presenting formidable treatment hurdles. The pressing need is to explore novel antibiotics to address this challenge. ShangKeHuangShui (SKHS), a patented traditional Chinese herbal formula, has gained widespread use in averting post-traumatic infections, but its biological effects remain incomplete understanding. This study's primary objective was to delve into the antibacterial properties, potential antibacterial compounds within SKHS, and their associated molecular targets. In vitro SKHS antibacterial assays demonstrated that the minimum inhibitory concentration (MIC) was 8.625 mg/mL and the minimum bactericide concentration (MBC) was 17.25 mg/mL. Proteomic analysis based on tandem mass tag (TMT) showed significant changes in the expression level of 246 proteins in SKHS treated group compared to control group, with 79 proteins upregulated and 167 proteins downregulated (>1.5-fold, p < 0.05). Subsequently, thirteen target proteins related to various biological processes and multiple metabolic pathways were selected to conduct parallel reaction monitoring (PRM) and molecular docking screen. In protein tyrosine phosphatase PtpA (ptpA) docking screening, phellodendrine and obacunone can bind to ptpA with the binding energy of 8.4 and 8.3 kcal/mol, respectively. This suggests their potential impact on antibacterial activity by modulating the two-component system of SAU. The discovery lays a groundwork for future research endeavors for exploring new antibacterial candidates and elucidating specific active chemical components within SKHS that match target proteins. Further investigations are imperative to unveil the biological effects of these monomers and their potential synergistic actions.

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Section: Discussionmentioning

confidence: 99%

Proteomic Analysis of <i>Staphylococcus aureus</i> Treated with ShangKeHuangShui

Liu,

Zhao,

Yang

et al. 2024

Biological & Pharmaceutical Bulletin

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“…The α subunit encoded by rpoA plays an important role in RNAP assembly since its dimerization is the first step in the sequential assembly of subunits to form the holoenzyme (112). This core enzyme is conserved across the bacterial kingdom, however members of the Firmicutes contain an additional δ (rpoE) subunit (113). The δ subunit is essential for cell survival when facing a competing strain in a changing environment, and although δ is not essential, it is vital for the cell's ability to rapidly adapt and survive in nature (114).…”

Section: Discussionmentioning

confidence: 99%

Bacillus subtilismaintains antibiofilm activity againstStaphylococcus aureusfollowing adaptive laboratory evolution

Leistikow,

Solis,

Khaled

et al. 2023

Preprint

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Quorum sensing interference has been touted as an ideal mechanism for the development of new anti-virulence therapies. Recent work has establishedBacillus subtilis6D1, a Gram-positive spore forming bacterium with probiotic qualities, produces metabolites that inhibitStaphylococcus aureusvirulence and biofilm formation via quorum sensing interference. However, it remains unknown how long-term exposure to these molecules driveS. aureusadaptation and evolution.S. aureusplanktonic cells and biofilms were propagated in the presence ofB. subtilis6D1 cell free extracts (CFE) for ~73 generations. Fitness, virulence, and antibiotic resistance assays of the ancestor and all evolved lineages revealed the emergence of treatment and lifestyle associated ecological traits. Compared to the ancestor and media-evolved lineages,S. aureuslineages evolved in the presence ofB. subtilis6D1 CFE were less competitive in a biofilm and exhibited increased phenotypic sensitivity to multiple antibiotics. Notably,B. subtilis6D1 CFE maintained its ability to inhibitS. aureusbiofilm growth and disassemble mature biofilm in all evolved lineages.S. aureuspopulations propagated in the presence of CFE acquired missense mutations in genes associated with plasmid-borne efflux systems and RNA polymerase. Furthermore, CFE-evolved lineages did not develop mutations in both competence and drug resistance pathways found in similarly evolved control lineages. Our data suggest long-term exposure to biofilm inhibitory molecules, like those produced byB. subtilis6D1, can reduceS. aureus’fitness in a biofilm and increase sensitivity to multiple antibiotics.

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“…The small ω subunit, namely rpoZ, plays key roles in subunit folding, complex assembly, and maintenance of transcriptional integrity [24]. The δ factor, rpoE, plays an essential role in RNA polymerase function in SAU [25]. The ablation of rpoE resulted in decreased transcription, protein synthesis, and pathogenicity [26].…”

Section: Discussionmentioning

confidence: 99%

TMT-based proteomic analysis of the antibiotic effects of ShangKeHuangShui against Straphylococcus aureus

Liu

Zhao

Yang

et al. 2021

Preprint

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Post-traumatic infection is a serious orthopedic trauma complication commonly caused by Staphylococcus aureus (SAU). ShangKeHuangShui, also known as Yellow Aqueous Concentrate of Traumatology Herbs (YACTH), is prepared from six Chinese herbal medicines, which has been used for decades in our hospital to prevent post-traumatic infection. In the present study, we investigated the in vitro antibacterial effects and underlying mechanism of YACTH against SAU. YACTH exhibited significant antibacterial activity against SAU with the minimum inhibitory concentration (MIC) of 8.625 mg/mL. Proteomic analysis based on Tandem mass tag (TMT) showed different protein expression levels in SAU under the YACTH and control conditions. Compared to the control group, the expression level of 490 proteins of YACTH treated group significantly changed (>1.2 fold, P <0.05). Biological informatics analysis showed that these differential proteins were widely involved in a variety of biological processes and multiple metabolic pathways. We then selected 26 target proteins to further conduct Parallel reaction monitoring (PRM). The results revealed that the 9 down-regulated proteins were mainly involved in RNA polymerase, oxidative phosphorylation, ABC transporter and glycolysis; whereas, the 17 up-regulated proteins are related to RNA degradation, mismatch repair and ribosome. In conclusion, YACTH, which contains the water-soluble components of six Chinese herbs, is first reported to exhibit antibacterial activity against SAU in vitro . The results provide novel insights into the antibacterial mechanisms of YACTH on protein networks, which may help us find new potential antibiotic targets.

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Biochemical and structural analyses reveal critical residues in δ subunit affecting its bindings to β′ subunit of Staphylococcus aureus RNA polymerase

Cited by 6 publications

References 21 publications

Proteomic Analysis of <i>Staphylococcus aureus</i> Treated with ShangKeHuangShui

Proteomic Analysis of <i>Staphylococcus aureus</i> Treated with ShangKeHuangShui

Bacillus subtilismaintains antibiofilm activity againstStaphylococcus aureusfollowing adaptive laboratory evolution

TMT-based proteomic analysis of the antibiotic effects of ShangKeHuangShui against Straphylococcus aureus

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