Whole-transcriptome analysis of oxidative stress response genes in carotenoid-producing Enterococcus gilvus

Metabolism of hydrogen peroxide by Lactobacillus plantarum NJAU-01: A proteomics study

This study aimed to investigate the time-course effect of Lactobacillus plantarum NJAU-01 in scavenging exogenous hydrogen peroxide (H₂O₂). The results showed that L. plantarum NJAU-01 at 10⁷ CFU/mL was able to eliminate a maximum of 4 mM H₂O₂ within a prolonged lag phase and resume to proliferate during the following culture. Redox state in the start-lag phase (0 h, without the addition of H₂O₂), indicated by glutathione and protein sulfhydryl, was impaired in the lag phase (3 h and 12 h) and then gradually recovered during subsequent growing stages (20 h and 30 h). By using sodium dodecyl sulfate-polyacrylamide gel electrophoresis and proteomics analysis, a total of 163 proteins such as PhoP family transcriptional regulator, glutamine synthetase, peptide methionine sulfoxide reductase, thioredoxin reductase, ribosomal proteins, acetolactate synthase, ATP binding subunit ClpX, phosphoglycerate kinase, UvrABC system protein A and UvrABC system protein B were identified as differential proteins across the entire growth phase. Those proteins were mainly involved in H₂O₂ sensing, protein synthesis, repairing proteins and DNA lesions, amino sugar and nucleotide sugar metabolism. Our data suggest that biomolecules of L. plantarum NJAU-01 are oxidized to passively consume H₂O₂ and are restored by the enhanced protein and/or gene repair systems.

The microbiome as a major function of the gastrointestinal tract and its implication in micronutrient metabolism and chronic diseases

The composition and function of microbes harbored in the human gastrointestinal lumen have been underestimated for centuries because of the underdevelopment of nucleotide sequencing techniques and the lack of humanized gnotobiotic models. Now, we appreciate that the gut microbiome is an integral part of the human body and exerts considerable roles in host health and diseases. Dietary factors can induce changes in the microbial community composition, metabolism, and function, thereby altering the host immune response, and consequently, may influence disease risks. An imbalance of gut microbiome homeostasis (i.e., dysbiosis) has been linked to several chronic diseases, such as inflammatory bowel diseases, obesity, and diabetes. Remarkable progress has recently been made in better understanding the extent to which the influence of the diet-microbiota interaction on host health outcomes in both animal models and human participants. However, the exact causality of the gut microbiome on the development of diseases is still controversial. In this review, we will briefly describe the general structure and function of the intestine and the process of nutrient absorption in humans. This is followed by a summarization of the recent updates on interactions between gut microbiota and individual micronutrients, including carotenoids, vitamin A, vitamin D, vitamin C, folate, iron, and zinc. In the opinion of the authors, these nutrients were identified as representative of vitamins and minerals with sufficient research on their roles in the microbiome. The host responses to the gut microbiome will also be discussed. Future direction in microbiome research, for example, precision microbiome, will be proposed.

Adaptive Response of Thermophiles to Redox Stress and Their Role in the Process of dye Degradation From Textile Industry Wastewater

Release of dye-containing textile wastewater into the environment causes severe pollution with serious consequences on aquatic life. Bioremediation of dyes using thermophilic microorganisms has recently attracted attention over conventional treatment techniques. Thermophiles have the natural ability to survive under extreme environmental conditions, including high dye concentration, because they possess stress response adaptation and regulation mechanisms. Therefore, dye detoxification by thermophiles could offer enormous opportunities for bioremediation at elevated temperatures. In addition, the processes of degradation generate reactive oxygen species (ROS) and subject cells to oxidative stress. However, thermophiles exhibit better adaptation to resist the effects of oxidative stress. Some of the major adaptation mechanisms of thermophiles include macromolecule repair system; enzymes such as superoxide dismutase, catalase, and glutathione peroxidase; and non-enzymatic antioxidants like extracellular polymeric substance (EPSs), polyhydroxyalkanoates (PHAs), etc. In addition, different bacteria also possess enzymes that are directly involved in dye degradation such as azoreductase, laccase, and peroxidase. Therefore, through these processes, dyes are first degraded into smaller intermediate products finally releasing products that are non-toxic or of low toxicity. In this review, we discuss the sources of oxidative stress in thermophiles, the adaptive response of thermophiles to redox stress and their roles in dye removal, and the regulation and crosstalk between responses to oxidative stress.

iTRAQ-based quantitative proteomic reveals proteomic changes in Serratia sp. CM01 and mechanism of Cr(Ⅵ) resistance

OBJECTIVE

Serratia sp. CM01 is a wild strain with the resistance and reduction ability of chromium(Ⅵ). The aim of this study it to investigate the underlying mechanisms of the Cr(Ⅵ) tolerance and reduction of strain CM01, and to explore its response to environmental pollution pressure at the molecular level.

METHODS

The iTRAQ technique was utilized to investigate the differentially expressed protein patterns related to the Cr(Ⅵ)-resistance in wild-type strain CM01 and domesticated CM01. RT-qPCR was used to verify the expression levels of several functional genes. The cell surface hydrophobicity and autoaggregation, the intracellular glucose content, and the total superoxide dismutase (SOD) activity were determined.

RESULTS

In total, 2750 proteins were detected and identified in WT CM01 and domesticated CM01. Compared with WT CM01, the iTRAQ results of 646 proteins were found to be significantly differentially expressed in domesticated CM01. There were 343 up-regulated and 303 down-regulated proteins, which mainly related to carbohydrate metabolism, stress responses, amino acid metabolism and some other systems. RT-qPCR results showed that the expression level of seven genes in domesticated CM01 were consistent with the iTRAQ proteomic profiles. The cell surface hydrophobicity, self-aggregation, intracellular glucose content and total SOD activity of domesticated CM01 with Cr(Ⅵ) treatment were significantly higher than without Cr(Ⅵ) treatment.

CONCLUSION

Domesticated CM01 displayed a complex biological network to exhibit the tolerance of Cr(Ⅵ), which may be attributed to the following aspects: (a) CM01 reduced the consumption of glucose by inhibiting the metabolism of carbohydrates, which was an energy-saving survival mode. (b) The inositol phosphate metabolism pathway played an important role. (c) Oxidative stress proteins enhanced the adaptability. (d) CM01 enhanced biosynthesis of hydrophobic amino acids to resistance to Cr(Ⅵ). (e) Several key systems and proteins, such as UvrABC system, Lon protease, porin OmpC, also may play an important role.

Transcriptome Analysis of Gene Expression in Dermacoccus abyssi HZAU 226 under Lysozyme Stress

Lysozyme acts as a kind of cationic antimicrobial protein and effectively hydrolyzes bacterial peptidoglycan to have a bactericidal effect, which also plays an important role in protecting eggs from microbial contamination. Dermacoccus abyssi HZAU 226, a Gram-positive bacterium isolated from spoiled eggs, has egg white and lysozyme tolerance, but its survival mechanism is unknown, especially from a transcriptomics point of view. In this study, the high lysozyme tolerance of D. abyssi HZAU 226 was characterized by three independent experiments, and then the Illumina RNA-seq was used to compare the transcriptional profiles of this strain in Luria–Bertani (LB) medium with and without 5 mg/mL lysozyme to identify differentially expressed genes (DEGs); 1024 DEGs were identified by expression analysis, including 544 up-regulated genes and 480 down-regulated genes in response to lysozyme treatment. The functional annotation analysis results of DEGs showed that these genes were mainly involved in glutathione biosynthesis and metabolism, ion transport, energy metabolism pathways, and peptidoglycan biosynthesis. This study is the first report of bacterial-related lysozyme RNA-seq, and our results help in understanding the lysozyme-tolerance mechanism of bacteria from a new perspective and provide transcriptome resources for subsequent research in related fields.

Complete Genome Sequence of Carotenoid-Producing Enterococcus gilvus CR1, Isolated from Raw Cow's Milk

Enterococcus gilvus CR1, isolated from raw cow's milk, can produce carotenoids. The complete genome sequence of this strain was determined using the PacBio RS II platform. The assembly was found to contain a circular chromosome, including carotenoid biosynthesis genes, and comprises 2,863,043 bp, with a G+C content of 41.86% and three plasmids.