Critical Minireview: The Fate of tRNACys during Oxidative Stress in Bacillus subtilis

Analysis of tRNA Cys processing under salt stress in Bacillus subtilis spore outgrowth using RNA sequencing data

Background: In spore-forming bacteria, the molecular mechanisms of accumulation of transfer RNA (tRNA) during sporulation must be a priority as tRNAs play an essential role in protein synthesis during spore germination and outgrowth. However, tRNA processing has not been extensively studied in these conditions, and knowledge of these mechanisms is important to understand long-term stress survival.    Methods:To gain further insight into tRNA processing during spore germination and outgrowth, the expression of the single copy tRNA ^Cys gene was analyzed in the presence and absence of 1.2 M NaCl in Bacillus subtilis using RNA-Seq data obtained from the Gene Expression Omnibus (GEO) database. The CLC Genomics work bench 12.0.2 (CLC Bio, Aarhus, Denmark, https://www.qiagenbioinformatics.com/) was used to analyze reads from the tRNA ^Cys gene.  Results:The results show that spores store different populations of tRNA ^Cys-related molecules.  One such population, representing 60% of total tRNA ^Cys, was composed of tRNA ^Cys fragments.  Half of these fragments (3´-tRF) possessed CC, CCA or incorrect additions at the 3´end. tRNA ^Cys with correct CCA addition at the 3´end represented 23% of total tRNA ^Cys, while with CC addition represented 9% of the total and with incorrect addition represented 7%. While an accumulation of tRNA ^Cys precursors was induced by upregulation of the rrnD operon under the control of  σ ^A -dependent promoters under both conditions investigated, salt stress produced only a modest effect on tRNA ^Cys expression and the accumulation of tRNA ^Cys related species. Conclusions:The results demonstrate that tRNA ^Cys molecules resident in spores undergo dynamic processing to produce functional molecules that may play an essential role during protein synthesis.

Deciphering the multicomponent synergy mechanisms of SiNiSan prescription on irritable bowel syndrome using a bioinformatics/network topology based strategy

BACKGROUND

SiNiSan (SNS) is a traditional Chinese medicine (TCM) prescription that has been widely used in the clinical treatment of irritable bowel syndrome (IBS). However, the underlying active substances and molecular mechanisms remain obscure.

PURPOSE

A bioinformatics/topology based strategy was proposed for identification of the drug targets, therapeutic agents and molecular mechanisms of SiNiSan against irritable bowel syndrome.

MATERIALS AND METHODS

In this work, a bioinformatics/network topology based strategy was employed by integrating ADME filtering, text mining, bioinformatics, network topology, Venn analysis and molecular docking to uncover systematically the multicomponent synergy mechanisms. In vivo experimental validation was executed in a Visceral Hypersensitivity (VHS) rat model.

RESULTS

76 protein targets and 109 active components of SNS were identified. Bioinformatics analysis revealed that 116 disease pathways associated with IBS therapy could be classified into the 19 statistically enriched functional sub-groups. The multi-functional co-synergism of SNS against IBS were predicted, including inflammatory reaction regulation, oxidative-stress depression regulation and hormone and immune regulation. The multi-component synergetic effects were also revealed on the herbal combination of SNS. The hub-bottleneck genes of the protein networks including PTGS2, CALM2, NOS2, SLC6A3 and MAOB, MAOA, CREB1 could become potential drug targets and Paeoniflorin, Naringin, Glycyrrhizic acid may be candidate agents. Experimental results showed that the potential mechanisms of SiNiSan treatment involved in the suppression of activation of Dopaminergic synapse and Amphetamine addiction signaling pathways, which are congruent with the prediction by the systematic approach.

CONCLUSION

The integrative investigation based on bioinformatics/network topology strategy may elaborate the multicomponent synergy mechanisms of SNS against IBS and provide the way out to develop new combination medicines for IBS.

Effect of ginger (Zingiber officinale) on semen quality

To date, according to the Scopus database, the biological effects of ginger (binominal name: Zingiber officinale), or ginger extracts, and its derived compounds on semen quality and sperm parameters have been revealed in more than 35 original articles. Though, still, there are no collective systematic or narrative discussion and conclusion of this specific research streak. Here, we systematically review and summarise the current link between ginger and its bioactive compounds with semen quality. To achieve this, we searched the central databases (Scopus and PubMed) for original studies, published in English language from August 2004 through February 2019 using the keywords "ginger" versus "sperm" and "semen." In summary, there is solid evidence that ginger enhances semen quality and improves the main sperm parameters such as concentration, viability, motility and morphology. Such beneficial effects of ginger on semen quality are attributable, at least in part, to increased levels of gonadal hormones, in particular, testosterone and luteinising hormone, decreased oxidative damage to cells, increased production of nitric oxide, hypoglycaemic response of ginger and the presence of valued nutrients in ginger such as manganese. Still, the positive effects of ginger on semen quality require additional approval in men.

Analysis of tRNACys processing in the absence of CCAase in Bacillus subtilis

In Bacillus subtilis, the tRNA^Cys lacks an encoded CCA 3' end. To gain insight into the role of CCAase and RNases in tRNA^Cys processing, several mutant strains were generated. Northern blot and RT-PCR results suggest that enzymes other than CCAase can participate in CCA addition at the 3' end of the immature tRNA^Cys.

Regulatory Factors for tRNA Modifications in Extreme- Thermophilic Bacterium Thermus thermophilus

Thermus thermophilus is an extreme-thermophilic bacterium that can grow at a wide range of temperatures (50-83°C). To enable T. thermophilus to grow at high temperatures, several biomolecules including tRNA and tRNA modification enzymes show extreme heat-resistance. Therefore, the modified nucleosides in tRNA from T. thermophilus have been studied mainly from the view point of tRNA stabilization at high temperatures. Such studies have shown that several modifications stabilize the structure of tRNA and are essential for survival of the organism at high temperatures. Together with tRNA modification enzymes, the modified nucleosides form a network that regulates the extent of different tRNA modifications at various temperatures. In this review, I describe this network, as well as the tRNA recognition mechanism of individual tRNA modification enzymes. Furthermore, I summarize the roles of other tRNA stabilization factors such as polyamines and metal ions.

Ginger and Testosterone

Enhancing and protecting testosterone production is one target for many scientists because of its crucial role as a primary sex hormone in males. Several in vivo trials have utilized different dietary supplements and medicinal plants to enhance testosterone production in males. Since 1991, various in-vivo, as well as basic research studies, have discovered a link between ginger (Zingiber officinale) and testosterone. However, such a link has not yet been collectively reviewed. This review systematically discusses and summarizes the effect of ginger and ginger extracts on testosterone. To achieve this contribution, we searched the PubMed, Scopus, and Web of Science databases for English language articles (full texts or abstracts) from November 1991 through August 2018 using the keywords "ginger" and "Zingiber officinale" versus "testosterone". Additionally, the references from related published articles were also reviewed, only if relevant. In conclusion, the mainstream of research that links ginger to testosterone demonstrated that ginger supplementation, particularly in oxidative stress conditions, enhances testosterone production in males. The mechanisms by which this occurs mainly by enhancing luteinizing hormone (LH) production, increasing the level of cholesterol in the testes, reducing oxidative stress and lipid peroxidation in the testes, enhancing the activity of the antioxidant enzymes, normalizing blood glucose, increasing blood flow in the testes, increasing testicular weight, and recycling testosterone receptors. However, the effect of ginger on testosterone is not yet confirmed in humans. Therefore, clinical studies in this context of research are imperative.

Role of Uric Acid in Semen

Since 1963, various research studies and reports have demonstrated the role of uric acid (2,6,8-trihydroxypurine), an end product of adenosine and guanosine catabolism, on semen quality and sperm function. However, this effect has not yet been collectively discussed, even though uric acid has been a well-recognized constituent in semen. Here, we systematically and comprehensively discuss and summarize the role/effect of uric acid in semen quality by searching the main databases for English language articles considering this topic. Additionally, certain significant and relevant papers were considered to support discussions and perceptions. In conclusion, uric acid contributes to maintaining and enhancing sperm motility, viability, and morphology; therefore, protecting sperm function and fertilizing ability. This contribution is performed mainly by neutralizing the damaging effect of oxidizing (e.g., endogenous free radicals and exogenous toxins) and nitrating agents and enhancing certain bioactive enzymes in spermatozoa. In contrast, high levels of uric acid may induce adverse effects to sperm function, at least in part, by reducing the activity of vital enzymes in spermatozoa. However, further research, mainly clinical, is still required to fully explore the role/effect of uric acid in semen.