The hypothetical YugA protein is involved in the positive regulation of galactose and maltose assimilation in L. lactis IL1403

Background: Osteoarthritis (OA), one of the most important causes leading to joint disability, was considered as an untreatable disease. A series of genes were reported to regulate the pathogenesis of OA, including microRNAs, Long non-coding RNAs and Circular RNA. So far, the expression profiles and functions of lncRNAs, mRNAs, and circRNAs in OA are not fully understood. Objective: The present study aimed to identify differently expressed genes in OA. Methods: The present study conducted RNA-seq to identify differently expressed genes in OA. Ontology (GO) analysis was used to analysis the Molecular Function and Biological Process. KEGG pathway analysis was used to perform the differentially expressed lncRNAs in biological pathways. Results: Hierarchical clustering revealed a total of 943 mRNAs, 518 lncRNAs, and 300 circRNAs were dysregulated in OA compared to normal samples. Furthermore, we constructed differentially expressed mRNAs mediated proteinprotein interaction network, differentially expressed lncRNAs mediated trans regulatory networks, and competitive endogenous RNA (ceRNA) to reveal the interaction among these genes in OA. Bioinformatics analysis revealed these dysregulated genes were involved in regulating multiple biological processes, such as wound healing, negative regulation of ossification, sister chromatid cohesion, positive regulation of interleukin-1 alpha production, sodium ion transmembrane transport, positive regulation of cell migration, and negative regulation of inflammatory response. To the best of our knowledge, this study for the first time revealed the expression pattern of mRNAs, lncRNAs and circRNAs in OA. Conclusion: This study provided novel information to validate these differentially expressed RNAs may be as possible biomarkers and targets in OA.

Download Full-text

Aberrant expression of HDL-bound microRNA induced by a high-fat diet in a pig model: implications in the pathogenesis of dyslipidaemia

BMC Cardiovascular Disorders ◽

10.1186/s12872-021-02084-5 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Guoyuan Sui ◽

Lianqun Jia ◽

Nan Song ◽

Dongyu Min ◽

Si Chen ◽

...

Keyword(s):

Real Time ◽

Real Time Pcr ◽

High Fat Diet ◽

Enrichment Analysis ◽

Diet Group ◽

High Fat ◽

Positive Regulation ◽

Aberrant Expression ◽

Balanced Diet ◽

Mirna Sequencing

Abstract Background A high-fat diet can affect lipid metabolism and trigger cardiovascular diseases. A growing body of studies has revealed the HDL-bound miRNA profiles in familial hypercholesterolaemia; in sharp contrast, relevant studies on high-fat diet-induced dyslipidaemia are lacking. In the current study, HDL-bound miRNAs altered by a high-fat diet were explored to offer some clues for elucidating their effects on the pathogenesis of dyslipidaemia. Methods Six pigs were randomly divided into two groups of three pigs each, namely, the high-fat diet and the balanced diet groups, which were fed a high-fat diet and balanced diet separately for six months. HDL was separated from plasma, which was followed by dissociation of the miRNA bound to HDL. miRNA sequencing of the isolated miRNA was performed to identify the differential expression profiles between the two groups, which was validated by real-time PCR. TargetScan, miRDB, and miRWalk were used for the prediction of genes targeted by the differential miRNAs. Results Compared with the balanced diet group, the high-fat diet group had significantly higher levels of TG, TC, LDL-C and HDL-C at six months. miRNA sequencing revealed 6 upregulated and 14 downregulated HDL-bound miRNAs in the high-fat diet group compared to the balanced diet group, which was validated by real-time PCR. GO enrichment analysis showed that dysregulated miRNAs in the high-fat diet group were associated with the positive regulation of lipid metabolic processes, positive regulation of lipid biosynthetic processes, and positive regulation of Ras protein signal transduction. Insulin resistance and the Ras signalling pathway were enriched in the KEGG pathway enrichment analysis. Conclusions Twenty HDL-bound miRNAs are significantly dysregulated in high-fat diet-induced dyslipidaemia. This study presents an analysis of a new set of HDL-bound miRNAs that are altered by a high-fat diet and offers some valuable clues for novel mechanistic insights into high-fat diet-induced dyslipidaemia. Further functional verification study using a larger sample size will be required.

Download Full-text

Regulation of Bacillus subtilis aprE Expression by glnA through Inhibition of scoC and σD-Dependent degR Expression

Journal of Bacteriology ◽

10.1128/jb.00049-09 ◽

2009 ◽

Vol 191 (9) ◽

pp. 3050-3058 ◽

Cited By ~ 12

Author(s):

Sadanobu Abe ◽

Ayako Yasumura ◽

Teruo Tanaka

Keyword(s):

Bacillus Subtilis ◽

Glutamine Synthetase ◽

Alkaline Protease ◽

Negative Regulator ◽

Negative Regulators ◽

Global Regulation ◽

Positive Regulation ◽

Expression Levels ◽

Negative Effect ◽

Positive Effect

ABSTRACT Expression of the gene for the extracellular alkaline protease (aprE) of Bacillus subtilis is subject to regulation by many positive and negative regulators. We have found that aprE expression was increased by disruption of the glutamine synthetase gene glnA. The increase in aprE expression was attributed to a decreased in expression of scoC, which encodes a negative regulator of aprE expression. The glnA effect on scoC expression was abolished by further disruption of tnrA, indicating that aprE expression is under global regulation through TnrA. In the scoC background, however, aprE expression was decreased by glnA deletion, and it was shown that the decrease was due to a defect in positive regulation by DegU. Among the genes that affect aprE expression through DegU, the expression of degR, encoding a protein that stabilizes phosphorylated DegU, was inhibited by glnA deletion. It was further shown that the decrease in degR expression by glnA deletion was caused by inhibition of the expression of sigD, encoding the σD factor, which is required for degR expression. In accordance with these findings, the expression levels of aprE-lacZ in glnA scoC degR and scoC degR strains were identical. These results led us to conclude that glnA deletion brings about two effects on aprE expression, i.e., a positive effect through inhibition of scoC expression and a negative effect through inhibition of degR expression, with the former predominating over the latter.

Download Full-text

Microcalorimetric study of the growth of bacterial colonies of Lactococcus lactis IL1403 in agar gels

Food Microbiology ◽

10.1016/j.fm.2011.08.018 ◽

2012 ◽

Vol 29 (1) ◽

pp. 67-79 ◽

Cited By ~ 32

Author(s):

N. Kabanova ◽

I. Stulova ◽

R. Vilu

Keyword(s):

Lactococcus Lactis ◽

Agar Gels ◽

Lactis Il1403

Download Full-text

Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli

Molecular Microbiology ◽

10.1046/j.1365-2958.2001.02380.x ◽

2001 ◽

Vol 40 (1) ◽

pp. 245-256 ◽

Cited By ~ 263

Author(s):

Bangdong L. Wei ◽

Anne-Marie Brun-Zinkernagel ◽

Jerry W. Simecka ◽

Birgit M. Prüß ◽

Paul Babitzke ◽

...

Keyword(s):

Escherichia Coli ◽

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Positive Regulation

Download Full-text

Positive Regulation of Corneal Type V Collagen mRNA: Analysis by Chicken–Human Heterokaryon Formation

Experimental Cell Research ◽

10.1006/excr.1996.0296 ◽

1996 ◽

Vol 228 (1) ◽

pp. 36-43 ◽

Cited By ~ 4

Author(s):

Thomas F. Linsenmayer ◽

Frank Igoe ◽

Eileen Gibney ◽

Marion K. Gordon ◽

David E. Birk

Keyword(s):

Positive Regulation ◽

Type V Collagen ◽

Collagen Mrna ◽

Heterokaryon Formation ◽

Mrna Analysis ◽

Type V

Download Full-text

82 Methyl Donor Supplementation Alters Cytosine Methylation and Biological Processes of Cells Cultured in Divergent Glucose Media Reflecting Improvements in Mitochondrial Respiration and Cell Growth Rate

Journal of Animal Science ◽

10.1093/jas/skab054.178 ◽

2021 ◽

Vol 99 (Supplement_1) ◽

pp. 109-109

Author(s):

Matthew S Crouse ◽

Wellison Jarles Da Silva Diniz ◽

Joel Caton ◽

Carl R Dahlen ◽

Lawrence P Reynolds ◽

...

Keyword(s):

Growth Rate ◽

Cell Proliferation ◽

Cell Growth ◽

Vitamin B12 ◽

Mitochondrial Respiration ◽

Cytosine Methylation ◽

Biological Processes ◽

Cell Growth Rate ◽

Metabolic Processes ◽

Positive Regulation

Abstract We hypothesized that supplementation of one-carbon metabolites (OCM: methionine, folate, choline, and vitamin B12) to bovine embryonic tracheal fibroblasts in divergent glucose media would alter cytosine methylation, and alterations in cytosine methylation will reflect biological processes matching previously improved mitochondrial respiration, cell proliferation, and cell growth rate data. Cells were cultured with 1g/L glucose (Low) or 4.5g/L glucose (High). Control medium (CON) contained basal concentrations of folate (0.001g/L), choline (0.001g/L), vitamin B12 (4µg/L), and methionine (0.015g/L). The OCM were supplemented at 2.5 and 5 times (2.5X and 5X, respectively) the CON media, except methionine was limited to 2X across all supplemented treatments. Cells were passaged three times in their treatment media before DNA extraction. Reduced representation bisulfite sequencing was adopted to analyze and compare the genomic methylation patterns within and across treatments using edgeR. Biological processes (BP) were retrieved based on the nearest genes of differentially methylated cytosines (P < 0.01) for each comparison between treatments. In both Low and High treatments, greater OCM increased the proportion of hypomethylated vs. hypermethylated cytosines. Functional analyses pointed out positive regulation of BP related to energy metabolism, except for the contrasts within the High group. Among the BP, we can highlight positive regulation of: GTPase activity, catalytic activity, molecular function, protein modification processes, phosphorylation, protein phosphorylation, cellular protein metabolic processes, MAPK cascade, and metabolic processes. These data support previously reported results from this experiment that showed increased mitochondrial respiration, cell proliferation, and growth rates with increasing OCM levels. We interpret these data to imply that when energy and OCM requirements are met for growth and basal methylation levels, DNA methylation levels decrease which may allow for greater transcription. Thus, OCM can be utilized for other functions such as polyamine synthesis, nucleotide synthesis, energetic metabolites, and phosphatidylcholine synthesis. USDA is an equal opportunity provider and employer.

Download Full-text