Comparative Proteomic Analysis of Propane Metabolism in Mycobacterium sp. Strain ENV421 and Rhodococcus sp. Strain ENV425

2018 ◽  
Vol 28 (3) ◽  
pp. 107-115 ◽  
Author(s):  
Peter Robert Tupa ◽  
Hisako Masuda
Keyword(s):  
Metabolic Pathways ◽  
Molecular Basis ◽  
Bacterial Species ◽  
Expression Patterns ◽  
Environmental Pollutants ◽  
Sole Source ◽  
Comparative Proteomic Analysis ◽  
Metabolic Versatility ◽  
Inducible Protein ◽  
Xenobiotic Degradation

While growing on propane as a sole source of carbon, many strains cometabolically degrade environmental pollutants, such as ethers and chlorinated hydrocarbons. To gain insights into the molecular basis behind such a high metabolic versatility of propanotrophs, we examined the propane-inducible protein expression patterns of 2 soil actinobacteria that are known to degrade a variety of ethers (i.e., <i>Mycobacterium</i> sp. strain ENV421 and <i>Rhodococcus</i> sp. strain ENV425). In both strains, soluble diiron monooxygenase(s), that would catalyze the first step of the pathway, were induced by propane. However, despite their phylogenetic similarity, different sets of additional putative propane oxygenases (e.g., cytochrome P450 and particulate methane monooxygenases) were overexpressed in the 2 strains. They also diverged in the expression of enzymes responsible for downstream reactions. This study revealed a diversity of expression of putative propane oxygenases, which may be responsible for xenobiotic degradation, as well as a variety of metabolic pathways for propane in these bacterial species.

scholarly journals Genome-wide characterization of 2-oxoglutarate and Fe(II)-dependent dioxygenase family genes in tomato during growth cycle and their roles in metabolism

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shuo Wei ◽  
Wen Zhang ◽  
Rao Fu ◽  
Yang Zhang
Keyword(s):  
Metabolic Pathways ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Growth Cycle ◽  
Model Organisms ◽  
Gibberellin Biosynthesis ◽  
Type I ◽  
Multiple Model ◽  
Genome Wide ◽  
Tomato Growth

Abstract Background 2-Oxoglutarate and Fe(II)-dependent dioxygenases (2ODDs) belong to the 2-oxoglutarate-dependent dioxygenase (2OGD) superfamily and are involved in various vital metabolic pathways of plants at different developmental stages. These proteins have been extensively investigated in multiple model organisms. However, these enzymes have not been systematically analyzed in tomato. In addition, type I flavone synthase (FNSI) belongs to the 2ODD family and contributes to the biosynthesis of flavones, but this protein has not been characterized in tomato. Results A total of 131 2ODDs from tomato were identified and divided into seven clades by phylogenetic classification. The Sl2ODDs in the same clade showed similar intron/exon distributions and conserved motifs. The Sl2ODDs were unevenly distributed across the 12 chromosomes, with different expression patterns among major tissues and at different developmental stages of the tomato growth cycle. We characterized several Sl2ODDs and their expression patterns involved in various metabolic pathways, such as gibberellin biosynthesis and catabolism, ethylene biosynthesis, steroidal glycoalkaloid biosynthesis, and flavonoid metabolism. We found that the Sl2ODD expression patterns were consistent with their functions during the tomato growth cycle. These results indicated the significance of Sl2ODDs in tomato growth and metabolism. Based on this genome-wide analysis of Sl2ODDs, we screened six potential FNSI genes using a phylogenetic tree and coexpression analysis. However, none of them exhibited FNSI activity. Conclusions Our study provided a comprehensive understanding of the tomato 2ODD family and demonstrated the significant roles of these family members in plant metabolism. We also suggest that no FNSI genes in tomato contribute to the biosynthesis of flavones.

scholarly journals Interaction of Azole-Based Environmental Pollutants with the Coelomic Hemoglobin from Amphitrite ornata: A Molecular Basis for Toxicity

Biochemistry ◽  
2017 ◽  
Vol 56 (17) ◽  
pp. 2294-2303 ◽  
Author(s):  
Nikolette L. McCombs ◽  
Tadeo Moreno-Chicano ◽  
Leiah M. Carey ◽  
Stefan Franzen ◽  
Michael A. Hough ◽  
...  
Keyword(s):  
Molecular Basis ◽  
Environmental Pollutants ◽  
Amphitrite Ornata

The liver proteome response to torpor in a basoendothermic mammal, Tenrec ecaudatus, provides insights into the evolution of homeothermy

2021 ◽  
Author(s):  
Jane I Khudyakov ◽  
Michael D Treat ◽  
Mikayla C Shanafelt ◽  
Jared S Deyarmin ◽  
Benjamin A Neely ◽  
...  
Keyword(s):  
Body Temperature ◽  
Metabolic Rate ◽  
Metabolic Pathways ◽  
Molecular Basis ◽  
Protein Abundance ◽  
Poor Control ◽  
High Body ◽  
Liver Proteome ◽  
The Common

Many mammals use adaptive heterothermy (e.g. torpor, hibernation) to reduce metabolic demands of maintaining high body temperature (Tb). Torpor is typically characterized by coordinated declines in Tb and metabolic rate (MR) followed by active rewarming. Most hibernators experience periods of euthermy between bouts of torpor during which homeostatic processes are restored. In contrast, the common tenrec, a basoendothermic Afrotherian mammal, hibernates without interbout arousals and displays extreme flexibility in Tb and MR. We investigated the molecular basis of this plasticity in tenrecs by profiling the liver proteome of animals that were active or torpid with high and more stable Tb (~32°C) or lower Tb (~14°C). We identified 768 tenrec liver proteins, of which 50.9% were differentially abundant between torpid and active animals. Protein abundance was significantly more variable in active cold and torpid compared to active warm animals, suggesting poor control of proteome abundance. Our data suggest that torpor in tenrecs may lead to mismatches in protein pools due to poor coordination of anabolic and catabolic processes. We propose that the evolution of endothermy leading to a more realized homeothermy of boreoeutherians likely led to greater coordination of homeostatic processes and reduced mismatches in thermal sensitivities of metabolic pathways.

scholarly journals Transcriptomic Analysis Reveals Candidate Genes Responsive to Sclerotinia scleroterum and Cloning of the Ss-Inducible Chitinase Genes in Morus laevigata

2020 ◽  
Vol 21 (21) ◽  
pp. 8358
Author(s):  
Huanhuan Jiang ◽  
Xiaoyun Jin ◽  
Xiaofeng Shi ◽  
Yufei Xue ◽  
Jiayi Jiang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Molecular Basis ◽  
Expression Patterns ◽  
Interaction Network ◽  
Sclerotinia Stem Rot ◽  
Response Characteristics ◽  
Kegg Pathways ◽  
Cdna Sequences ◽  
Chitinase Genes ◽  
Morus Laevigata

Sclerotinia sclerotiorum (Ss) is a devastating fungal pathogen that causes Sclerotinia stem rot in rapeseed (Brassica napus), and is also detrimental to mulberry and many other crops. A wild mulberry germplasm, Morus laevigata, showed high resistance to Ss, but the molecular basis for the resistance is largely unknown. Here, the transcriptome response characteristics of M. laevigata to Ss infection were revealed by RNA-seq. A total of 833 differentially expressed genes (DEGs) were detected after the Ss inoculation in the leaf of M. laevigata. After the GO terms and KEGG pathways enrichment analyses, 42 resistance-related genes were selected as core candidates from the upregulated DEGs. Their expression patterns were detected in the roots, stems, leaves, flowers, and fruits of M. laevigata. Most of them (30/42) were specifically or mainly expressed in flowers, which was consistent with the fact that Ss mainly infects plants through floral organs, and indicated that Ss-resistance genes could be induced by pathogen inoculation on ectopic organs. After the Ss inoculation, these candidate genes were also induced in the two susceptible varieties of mulberry, but the responses of most of them were much slower with lower extents. Based on the expression patterns and functional annotation of the 42 candidate genes, we cloned the full-length gDNA and cDNA sequences of the Ss-inducible chitinase gene set (MlChi family). Phylogenetic tree construction, protein interaction network prediction, and gene expression analysis revealed their special roles in response to Ss infection. In prokaryotic expression, their protein products were all in the form of an inclusion body. Our results will help in the understanding of the molecular basis of Ss-resistance in M. laevigata, and the isolated MlChi genes are candidates for the improvement in plant Ss-resistance via biotechnology.

scholarly journals Role of bacteria in oral carcinogenesis

2012 ◽  
Vol 01 (02) ◽  
pp. 78-83 ◽  
Author(s):  
R Rajeev ◽  
Kanaram Choudhary ◽  
Swagatika Panda ◽  
Neha Gandhi
Keyword(s):  
Metabolic Pathways ◽  
Bacterial Species ◽  
Cancer Therapeutics ◽  
Microbial Populations ◽  
Genetic Mutations ◽  
Oral Carcinogenesis ◽  
Common Cancer ◽  
Indian Men ◽  
Oral Microorganisms

AbstractOral cancer is the most common cancer diagnosed in Indian men and is the leading cause of cancer deaths. It is considered as a multistep and multifactorial disease. Besides accumulation of genetic mutations, numerous other carcinogens are involved. In this category, viral and chemical carcinogens are well studied and documented. However, in the oral cavity, the role of microbiota in carcinogenesis is not known. Microbial populations on mouth mucosa differ between healthy and malignant sites, and certain oral bacterial species have been linked with malignancies, but the evidence is still weak in this respect. Nevertheless, oral microorganisms inevitably up-regulate cytokines and other inflammatory mediators that affect the complex metabolic pathways, and may thus be involved in carcinogenesis. Poor oral health associates statistically with prevalence of many types of cancer such as pancreatic and gastrointestinal cancer. This review presents possible carcinogenesis pathway involved in bacterial carcinogenesis, commonly implicated bacteria in oral carcinogenesis, and their role in cancer therapeutics as well.

Comparative proteomic analysis of hybrid maize MR2008 and its parental lines

2021 ◽  
Vol 159 (7-8) ◽  
pp. 570-579
Author(s):  
E. E. Osawa-Martínez ◽  
B. Minjarez ◽  
Y. Rodríguez-Yáñez ◽  
E. E. Reza-Zaldivar ◽  
A. A. Canales-Aguirre ◽  
...  
Keyword(s):  
Quality Control ◽  
Metabolic Pathways ◽  
New Technologies ◽  
Bioinformatics Analysis ◽  
Agricultural Practices ◽  
White Variety ◽  
Comparative Proteomic Analysis ◽  
The World ◽  
Parental Lines ◽  
Hybrid Maize

AbstractMaize is one of the three staple foods in the world. The white variety represents 60% of the maize importation with a world consumption of 1125 million tons in 2019/2020. Currently, new technologies could contribute to the analysis of this seed, supporting quality control and improvement. This study aims to carry out the morphological and proteomic comparison between the hybrid MR2008 and its parental lines LUG03 and CML491 through mass spectrometry and bioinformatics analysis. Herein, we identified that 34.8% of the hybrid proteome differs from the parental proteome. Also, ontological and morphological analyses determined that the hybrid exhibits more characteristics related to CML491 than LUG03, for example, metabolic pathways and enzymes, such as anthocyanidin 3-O-glucosyltransferase (UniProt P16166). This analysis allowed the identification of dominant characters, metabolic pathways and confirms the utility of this methodology in agricultural practices, mainly in processes of selection and quality control of a crop.

scholarly journals Maternal and Post-weaning High-Fat Diets Produce Distinct DNA Methylation Patterns in Hepatic Metabolic Pathways within Specific Genomic Contexts

2019 ◽  
Vol 20 (13) ◽  
pp. 3229 ◽  
Author(s):  
Moody ◽  
Wang ◽  
Jung ◽  
Chen ◽  
Pan
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Metabolic Pathways ◽  
Expression Patterns ◽  
Sprague Dawley ◽  
High Fat ◽  
Differentially Methylated Genes ◽  
High Fat Diets ◽  
Diet Intake ◽  
Fat Diets

Calorie-dense high-fat diets (HF) are associated with detrimental health outcomes, including obesity, cardiovascular disease, and diabetes. Both pre- and post-natal HF diets have been hypothesized to negatively impact long-term metabolic health via epigenetic mechanisms. To understand how the timing of HF diet intake impacts DNA methylation and metabolism, male Sprague–Dawley rats were exposed to either maternal HF (MHF) or post-weaning HF diet (PHF). At post-natal week 12, PHF rats had similar body weights but greater hepatic lipid accumulation compared to the MHF rats. Genome-wide DNA methylation was evaluated, and analysis revealed 1744 differentially methylation regions (DMRs) between the groups with the majority of the DMR located outside of gene-coding regions. Within differentially methylated genes (DMGs), intragenic DNA methylation closer to the transcription start site was associated with lower gene expression, whereas DNA methylation further downstream was positively correlated with gene expression. The insulin and phosphatidylinositol (PI) signaling pathways were enriched with 25 DMRs that were associated with 20 DMGs, including PI3 kinase (Pi3k), pyruvate kinase (Pklr), and phosphodiesterase 3 (Pde3). Together, these results suggest that the timing of HF diet intake determines DNA methylation and gene expression patterns in hepatic metabolic pathways that target specific genomic contexts.

scholarly journals Approaches and perspectives to toxicogenetics and toxicogenomics

2015 ◽  
Vol 62 (4) ◽  
pp. 605-615 ◽  
Author(s):  
Ana Lucia Castiblanco Rodriguez
Keyword(s):  
Molecular Basis ◽  
Environmental Pollutants ◽  
Predictive Toxicology ◽  
Toxic Response ◽  
Mechanisms Of Toxicity ◽  
Biomarkers Of Exposure ◽  
Scientific Disciplines ◽  
Toxic Agents ◽  
Chemical Products ◽  
Genomic Response

Toxicology is one of the scientific disciplines that has most<br />evolved in recent years due to scientific and technological<br />advances that have created a deeper understanding of the<br />genetic and molecular basis for appreciative variability in<br />toxic response from one person to another. The application<br />of this knowledge in toxicology is known as toxicogenetics<br />and toxicogenomics. The latter is the discipline that studies<br />the genomic response of organisms exposed to chemical<br />agents, including drugs, environmental pollutants, food<br />additives, and other commonly used chemical products.<br />The use of emerging omic technologies, such as genomics,<br />transcriptomics, proteomics, metabolomics and bioinformatics<br />techniques, permits the analysis of many variants of genes<br />simultaneously in an organism exposed to toxic agents in order<br />to search for genes susceptible to damage, to detect patterns<br />and mechanisms of toxicity, and determine specific profiles<br />of gene expression that give origin to biomarkers of exposure<br />and risk. This constitutes predictive toxicology.

scholarly journals Heterozygous, Polyploid, Giant Bacterium, Achromatium, Possesses an Identical Functional Inventory Worldwide across Drastically Different Ecosystems

2020 ◽  
Author(s):  
Danny Ionescu ◽  
Luca Zoccarato ◽  
Artur Zaduryan ◽  
Sina Schorn ◽  
Mina Bizic ◽  
...  
Keyword(s):  
Species Concept ◽  
Single Cells ◽  
Bacterial Species ◽  
Expression Patterns ◽  
Allelic Diversity ◽  
Evolutionary Mechanisms ◽  
Genomic Features ◽  
Bacterial Speciation ◽  
Depth Ranges ◽  
Functional Versatility

Abstract Achromatium is large, hyperpolyploid and the only known heterozygous bacterium. Single cells contain approximately 300 different chromosomes with allelic diversity far exceeding that typically harbored by single bacteria genera. Surveying all publicly available sediment sequence archives, we show that Achromatium is common worldwide, spanning temperature, salinity, pH, and depth ranges normally resulting in bacterial speciation. Although saline and freshwater Achromatium spp. appear phylogenetically separated, the genus Achromatium contains a globally identical, complete functional inventory regardless of habitat. Achromatium spp. cells from differing ecosystems (e.g., from freshwater to saline) are, unexpectedly, equally functionally equipped but differ in gene expression patterns by transcribing only relevant genes. We suggest that environmental adaptation occurs by increasing the copy number of relevant genes across the cell’s hundreds of chromosomes, without losing irrelevant ones, thus maintaining the ability to survive in any ecosystem type. The functional versatility of Achromatium and its genomic features reveal alternative genetic and evolutionary mechanisms, expanding our understanding of the role and evolution of polyploidy in bacteria while challenging the bacterial species concept and drivers of bacterial speciation.

scholarly journals Time Series RNA-seq in Pigeonpea Revealed the Core Genes in Metabolic Pathways under Aluminum Stress

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 380 ◽  
Author(s):  
Zhaoxu Gao ◽  
Biying Dong ◽  
Hongyan Cao ◽  
Hang He ◽  
Qing Yang ◽  
...  
Keyword(s):  
Time Series ◽  
Metabolic Pathways ◽  
Expression Patterns ◽  
Plant Stress ◽  
Regulation Mechanism ◽  
Rna Seq ◽  
Aluminum Stress ◽  
Biological Regulation ◽  
Al Stress ◽  
The Impact

Pigeonpea is an important economic crop in the world and is mainly distributed in tropical and subtropical regions. In order to further expand the scope of planting, one of the problems that must be solved is the impact of soil acidity on plants in these areas. Based on our previous work, we constructed a time series RNA sequencing (RNA-seq) analysis under aluminum (Al) stress in pigeonpea. Through a comparison analysis, 11,425 genes were found to be differentially expressed among all the time points. After clustering these genes by their expression patterns, 12 clusters were generated. Many important functional pathways were identified by gene ontology (GO) analysis, such as biological regulation, localization, response to stimulus, metabolic process, detoxification, and so on. Further analysis showed that metabolic pathways played an important role in the response of Al stress. Thirteen out of the 23 selected genes related to flavonoids and phenols were downregulated in response to Al stress. In addition, we verified these key genes of flavonoid- and phenol-related metabolism pathways by qRT-PCR. Collectively, our findings not only revealed the regulation mechanism of pigeonpea under Al stress but also provided methodological support for further exploration of plant stress regulation mechanisms.

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