The essential iron-sulphur protein Rli1 is a key determinant of oxidative stress resistance in Saccharomyces cerevisiae

Reactive oxygen species (ROS) are linked to a range of degenerative conditions in humans, and may cause damage to an array of cellular components. However, it is unclear which cellular target(s) of ROS may primarily account for toxicity during oxidative stress. The sensitivity of iron-sulphur (Fe-S) clusters to ROS makes these candidate determinants of ROS mediated cell killing. Ribonuclease L inhibitor (Rli1p) is a highly conserved protein that is essential in all tested eukaryotes and archaea, but requires Fe-S clusters for its crucial functions in protein synthesis. Herein, the novel hypothesis that ROS toxicity is caused by loss of Rli1p function was tested. Rli1p activity (in nuclear export of ribosomal subunits) was impaired during mild oxidative stress in yeast. In addition, resistance to pro-oxidants was decreased by RLI1 repression and increased by RLI1 overexpression. This Rli1p-dependency was abolished during anaerobicity and accentuated in cells expressing the Fe-S cluster defective Rli1p construct, rli1C58A. The effects appeared specific to Rli1p as overexpression of other essential Fe-S proteins did not increase stress resistance. Methionine sulphoxide reductases (MSRs) and the Mn-superoxide dismutase (Sod2p) are known to help preserve the integrity of Fe-S clusters in cells. Here, these proteins’ antioxidant actions were shown to be at least partly mediated through Rli1p. Resistance to both chronic and acute oxidative stress was Rli1p-dependent. Further experiments indicated that Rli1p-dependent protein synthesis could be a critical target of ROS and, specifically, that Rli1p function may help to protect against ROS-induced mRNA mistranslation. The study indicated that Rli1p function is a primary biological target of ROS action, owing to its essential nature but dependency on ROS-labile Fe-S clusters. Such insights could offer new approaches for combating oxidative stress-related disease

The essential iron-sulphur protein Rli1 is a key determinant of oxidative stress resistance in Saccharomyces cerevisiae

Reactive oxygen species (ROS) are linked to a range of degenerative conditions in humans, and may cause damage to an array of cellular components. However, it is unclear which cellular target(s) of ROS may primarily account for toxicity during oxidative stress. The sensitivity of iron-sulphur (Fe-S) clusters to ROS makes these candidate determinants of ROS mediated cell killing. Ribonuclease L inhibitor (Rli1p) is a highly conserved protein that is essential in all tested eukaryotes and archaea, but requires Fe-S clusters for its crucial functions in protein synthesis. Herein, the novel hypothesis that ROS toxicity is caused by loss of Rli1p function was tested. Rli1p activity (in nuclear export of ribosomal subunits) was impaired during mild oxidative stress in yeast. In addition, resistance to pro-oxidants was decreased by RLI1 repression and increased by RLI1 overexpression. This Rli1p-dependency was abolished during anaerobicity and accentuated in cells expressing the Fe-S cluster defective Rli1p construct, rli1C58A. The effects appeared specific to Rli1p as overexpression of other essential Fe-S proteins did not increase stress resistance. Methionine sulphoxide reductases (MSRs) and the Mn-superoxide dismutase (Sod2p) are known to help preserve the integrity of Fe-S clusters in cells. Here, these proteins’ antioxidant actions were shown to be at least partly mediated through Rli1p. Resistance to both chronic and acute oxidative stress was Rli1p-dependent. Further experiments indicated that Rli1p-dependent protein synthesis could be a critical target of ROS and, specifically, that Rli1p function may help to protect against ROS-induced mRNA mistranslation. The study indicated that Rli1p function is a primary biological target of ROS action, owing to its essential nature but dependency on ROS-labile Fe-S clusters. Such insights could offer new approaches for combating oxidative stress-related disease

The Anti-Colon Cancer Effects of Probiotic and Postbiotic: A Review Article

Cancer, the leading cause of death worldwide, is a name for more than 100 types of diseases that evolved from normal cells and tissues in the body. Cancer cells fail to control cell proliferation and homeostasis due to mutations. These mutations arise from intensive environmental factors or alterations in genes that aid genetic instability. The immune system is the first defense line against cancer cells as it inhibits tumor development, growth, invasion, and metastasis. However, cancer cells develop many mechanisms to escape and avoid destruction by the immune system. Probiotics is a term used to describe the entire population of microorganisms that inhabit the human body. Probiotics and their metabolites stimulate the immune system and maintain gastrointestinal integrity. Postbiotics are bioactive products produced by probiotics. They facilitate cell-cell interaction and regulate signaling pathways. Postbiotics also promote health through different mechanisms. In this review, the anti-colon-cancer effects of probiotics and postbiotics have been investigated

Transcriptional analysis of Rhazya stricta in response to jasmonic acid

Background: Jasmonic acid (JA) is a signal transducer molecule that plays an important role in plant development and stress response; it can also efficiently stimulate secondary metabolism in plant cells. Results: RNA-Seq technology was applied to identify differentially expressed genes and study the time course of gene expression in Rhazya stricta in response to JA. Of more than 288 million total reads, approximately 27% were mapped to genes in the reference genome. Genes involved during the secondary metabolite pathways were up- or downregulated when treated with JA in R. stricta. Functional annotation and pathway analysis of all up- and downregulated genes identified many biological processes and molecular functions. Jasmonic acid biosynthetic, cell wall organization, and chlorophyll metabolic processes were upregulated at days 2, 6, and 12, respectively. Similarly, the molecular functions of calcium-transporting ATPase activity, ADP binding, and protein kinase activity were also upregulated at days 2, 6, and 12, respectively. Time-dependent transcriptional gene expression analysis showed that JA can induce signaling in the phenylpropanoid and aromatic acid pathways. These pathways are responsible for the production of secondary metabolites, which are essential for the development and environmental defense mechanism of R. stricta during stress conditions. Conclusions: Our results suggested that genes involved in flavonoid biosynthesis and aromatic acid synthesis pathways were upregulated during JA stress. However, monoterpenoid indole alkaloid (MIA) was unaffected by JA treatment. Hence, we can postulate that JA plays an important role in R. stricta during plant development and environmental stress conditions. How to cite: Hajrah, NH, Rabah SO, Alghamdi MK, et al. Transcriptional analysis of Rhazya stricta in response to jasmonic acid. Electron J Biotechnol 2021;50. https://doi.org/10.1016/j.ejbt.2021.01.00

Data from: Plastome sequencing of ten nonmodel crop species uncovers a large insertion of mitochondrial DNA in cashew

In plant evolution, intracellular gene transfer (IGT) is a prevalent, ongoing process. While nuclear and mitochondrial genomes are known to integrate foreign DNA via IGT and horizontal gene transfer (HGT), plastid genomes (plastomes) have resisted foreign DNA incorporation and only recently has IGT been uncovered in the plastomes of a few land plants. In this study, we completed plastome sequences for l0 crop species and describe a number of structural features including variation in gene and intron content, inversions, and expansion and contraction of the inverted repeat (IR). We identified a putative rpl22 in cinnamon (Cinnamomum verum J. Presl) and other sequenced Lauraceae and an apparent functional transfer of rpl23 to the nucleus of quinoa (Chenopodium quinoa Willd.). In the orchard tree cashew (Anacardium occidentale L.), we report the insertion of an ∼6.7-kb fragment of mitochondrial DNA into the plastome IR. BLASTn analyses returned high identity hits to mitogenome sequences including an intact ccmB open reading frame. Using three plastome markers for five species of Anacardium, we generated a phylogeny to investigate the distribution and timing of the insertion. Four species share the insertion, suggesting that this event occurred <20 million yr ago in a single clade in the genus. Our study extends the observation of mitochondrial to plastome IGT to include long-lived tree species. While previous studies have suggested possible mechanisms facilitating IGT to the plastome, more examples of this phenomenon, along with more complete mitogenome sequences, will be required before a common, or variable, mechanism can be elucidated

AOE_Mt-K101-22contigs

Mitochondrial contigs of Anacardium occidentale (Cashew) assembled by Velvet assembler with a 101 kmer size

Next generation sequencing shows diversity of Omicron sub-lineages of SARS-COV2 circulating in Jeddah, Saudi Arabia

The ever-evolving Omicron variant of the SARS-CoV-2 and its sub-lineages have prompted Saudi Arabia to continuously track circulating lineages. We focused on the presence of diverse SARS-CoV-2 circulation in Saudi Arabia and presented the whole genome sequencing study of 94 positive SARS-CoV-2 specimens procured between February and April 2022 in the city of Jeddah, Saudi Arabia. Following whole-genome sequencing, bioinformatics analysis was undertaken. The SARS-CoV-2 variant Omicron clades 21K and 21L constituted the entirety of sequenced specimens, belonging to BA.2 (n = 56) and BA.1.1 (n = 20), respectively, and low-frequency sub-lineages were BA.2.3 (n = 6), BA.1 (n = 4), BA.2.40.1 (n = 2), BA.1.14 (n = 1), BA.2.10 (n = 1), BA2.32 (n = 1), BA.2.57 (n = 1), BA2.64 (n = 1), and BA2.5 (n = 1). Mutational patterns were identified, as well as possible consequences for the spread of the virus. Comparative molecular docking of Omicron-specific Nucleocapsid protein harboring the mutations P13L, R203K, G204R, as well as S413R, and the deletions E31-, R32-, and S33- showed reduced interaction with human RIG-I protein with 8 interacting amino acid residues and 10 polar interactions, while the SARS-CoV-2 Nucleocapsid protein exhibited 15 interacting amino acid residues and 26 polar interactions. Ongoing monitoring is essential for assessing the genomic epidemiological consequences of tourist travel and pilgrimage in Jeddah and across Saudi Arabia, as well as the prompt identification of emerging variants for further investigation

Plastome Sequencing of Ten Nonmodel Crop Species Uncovers a Large Insertion of Mitochondrial DNA in Cashew

In plant evolution, intracellular gene transfer (IGT) is a prevalent, ongoing process. While nuclear and mitochondrial genomes are known to integrate foreign DNA via IGT and horizontal gene transfer (HGT), plastid genomes (plastomes) have resisted foreign DNA incorporation and only recently has IGT been uncovered in the plastomes of a few land plants. In this study, we completed plastome sequences for l0 crop species and describe a number of structural features including variation in gene and intron content, inversions, and expansion and contraction of the inverted repeat (IR). We identified a putative in cinnamon ( J. Presl) and other sequenced Lauraceae and an apparent functional transfer of to the nucleus of quinoa ( Willd.). In the orchard tree cashew ( L.), we report the insertion of an ∼6.7-kb fragment of mitochondrial DNA into the plastome IR. BLASTn analyses returned high identity hits to mitogenome sequences including an intact open reading frame. Using three plastome markers for five species of , we generated a phylogeny to investigate the distribution and timing of the insertion. Four species share the insertion, suggesting that this event occurred <20 million yr ago in a single clade in the genus. Our study extends the observation of mitochondrial to plastome IGT to include long-lived tree species. While previous studies have suggested possible mechanisms facilitating IGT to the plastome, more examples of this phenomenon, along with more complete mitogenome sequences, will be required before a common, or variable, mechanism can be elucidated

Supplementary Information for the evolution of the plastid genomes in diatoms

This file contains supplementary information for the book chapter. Table A to G contains additional information of the genome size, genome rearrangement, and correlation between genome rearrangement etc