Catabolic Genes
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2021 ◽  
Vol 22 (15) ◽  
pp. 8202
Author(s):  
Ali Mohamed Elyamine ◽  
Jie Kan ◽  
Shanshan Meng ◽  
Peng Tao ◽  
Hui Wang ◽  
...  

Microbial biodegradation is one of the acceptable technologies to remediate and control the pollution by polycyclic aromatic hydrocarbon (PAH). Several bacteria, fungi, and cyanobacteria strains have been isolated and used for bioremediation purpose. This review paper is intended to provide key information on the various steps and actors involved in the bacterial and fungal aerobic and anaerobic degradation of pyrene, a high molecular weight PAH, including catabolic genes and enzymes, in order to expand our understanding on pyrene degradation. The aerobic degradation pathway by Mycobacterium vanbaalenii PRY-1 and Mycobactetrium sp. KMS and the anaerobic one, by the facultative bacteria anaerobe Pseudomonas sp. JP1 and Klebsiella sp. LZ6 are reviewed and presented, to describe the complete and integrated degradation mechanism pathway of pyrene. The different microbial strains with the ability to degrade pyrene are listed, and the degradation of pyrene by consortium is also discussed. The future studies on the anaerobic degradation of pyrene would be a great initiative to understand and address the degradation mechanism pathway, since, although some strains are identified to degrade pyrene in reduced or total absence of oxygen, the degradation pathway of more than 90% remains unclear and incomplete. Additionally, the present review recommends the use of the combination of various strains of anaerobic fungi and a fungi consortium and anaerobic bacteria to achieve maximum efficiency of the pyrene biodegradation mechanism.


2021 ◽  
Vol 11 (9) ◽  
pp. 4249
Author(s):  
Witchulada Yungyuen ◽  
Thi Thuong Vo ◽  
Apiradee Uthairatanakij ◽  
Gang Ma ◽  
Lancui Zhang ◽  
...  

Carotenoids are considered to be important components in mango fruits. However, there is a lack of understanding about the regulation of carotenoids in mango. To gain an insight into the carotenoid metabolism pathway, carotenoid content and the expression of carotenoid metabolic genes were investigated in the peel and pulp of mango during fruit development and ripening in three cultivars, ‘Kaituk’, ‘Nam Dok Mai No.4′, and ‘Nam Dok Mai Sithong’, which are different in color. The highest carotenoid content was observed in ‘Kaituk’, followed by ‘Nam Dok Mai No.4′ and ‘Nam Dok Mai Sithong’, with the major carotenoid being β-carotene. The gene expression analysis found that carotenoid metabolism in mango fruit was primarily regulated at the transcriptional level. The changing patterns of carotenoid biosynthetic gene expression (MiPSY, MiPDS, MiZDS, MiCRTISO, MiLCYb, MiLCYe, MiHYb, and MiZEP) were similar to carotenoid accumulation, and ‘Kaituk’ exhibited a higher expression level than the other two cultivars. In addition, the differential regulation of carotenoid catabolic genes was found to be a mechanism responsible for variability in carotenoid content among the three mango cultivars. The expression of carotenoid catabolic genes (MiCCD1, MiNCED2, and MiNCED3) more rapidly decreased in ‘Kaituk’, resulting in a larger amount of carotenoids in ‘Kaituk’ than the other two cultivars.


Author(s):  
Junwei Huang ◽  
Dian Chen ◽  
Xiangkun Kong ◽  
Shurui Wu ◽  
Kai Chen ◽  
...  

1-Naphthol, a widely used raw material for organic synthesis, is also a well-known organic pollutant. Due to its high toxicity, 1-naphthol is rarely used by microorganisms as the sole carbon source for growth. In this study, catabolism of 1-naphthol by Sphingobium sp. strain B2 was found to be greatly enhanced by additional supplementation with primary carbon sources (e.g., glucose, maltose and sucrose), and 1-naphthol was even used as the carbon source for growth when strain B2 cells had been pre-induced by both 1-naphthol and glucose. A distinct two-component flavin-dependent monooxygenase NdcA1A2 was found to be responsible for the initial hydroxylation of 1-naphthol to 1,2-dihydroxynaphthalene, a more toxic compound. Transcriptional levels of ndcA1A2 genes were significantly up-regulated when strain B2 cells were cultured with both 1-naphthol and glucose as compared to cells cultured with sole 1-naphthol or glucose. Two transcriptional regulators, the activator NdcS and the inhibitor NdcR were found to play key roles in the synergistic regulation of the transcription of the 1-naphthol initial catabolic genes ndcA1A2. Importance Co-metabolism is a widely observed phenomenon, especially in the field of microbial catabolism of highly toxic xenobiotics. However, the mechanisms of co-metabolism are ambiguous and the roles of the obligately co-existing growth substrates remain largely unknown. In this study, we revealed that the roles of the co-existing primary carbon sources (e.g. glucose) in the enhanced catabolism of the toxic compound 1-naphthol in Sphingobium sp. strain B2 was not solely because they were used as growth substrates to support cell growth, but more importantly they acted as “co-inducers” to interact with two transcriptional regulators, the activator NdcS and the inhibitor NdcR, to synergistically regulate the transcription of the 1-naphthol initial catabolic genes ndcA1A2. Our findings provide new insights into the co-metabolic mechanism of highly toxic compounds in microorganisms.


Author(s):  
Shunyao Li ◽  
Kai Sun ◽  
Xin Yan ◽  
Chao Lu ◽  
Michael Gatheru Waigi ◽  
...  
Keyword(s):  

2021 ◽  
Author(s):  
Junhui Li ◽  
Chongjian Jia ◽  
Qihong Lu ◽  
Bruce A Hungate ◽  
Paul Dijkstra ◽  
...  

Even though microbial communities can be more effective at degrading xenobiotics than cultured micro-organisms, yet little is known about the microbial strategies that underpin xenobiotic biodegradation by microbial communities. Here, we employ metagenomic community sequencing to explore the mechanisms that drive the development of 49 xenobiotic-degrading microbial communities, which were enriched from 7 contaminated soils or sediments with a range of xenobiotic compounds. We show that multiple microbial strategies likely co-drive the development of xenobiotic degrading communities, notably (i) presence of genes encoding catabolic enzymes to degrade xenobiotics; (ii) presence of genes encoding efflux pumps; (iii) auxiliary catabolic genes on plasmids; and (iv) positive interactions dominate microbial communities with efficient degradation. Overall, the integrated analyses of microbial ecological strategies advance our understanding of microbial processes driving the biodegradation of xenobiotics and promote the design of bioremediation systems.


2021 ◽  
Vol 12 ◽  
Author(s):  
Lin Zhu ◽  
Nana Qian ◽  
Yujun Sun ◽  
Xiaoming Lu ◽  
Haiming Duan ◽  
...  

Plants can naturally interact with beneficial rhizobacteria to mediate defense responses against foliar pathogen infection. However, the mechanisms of rhizobacteria-mediated defense enhancement remain rarely clear. In this study, beneficial rhizobacterial strain Pseudomonas fluorescens DN16 greatly increased the resistance of cucumber plants against Botrytis cinerea infection. RNA-sequencing analyses showed that several polyamine-associated genes including a thermospermine (TSpm) synthase gene (CsACL5) and polyamine catabolic genes (CsPAO1, CsPAO5, and CsCuAO1) were notably induced by DN16. The associations of TSpm metabolic pathways with the DN16-mediated cucumber defense responses were further investigated. The inoculated plants exhibited the increased leaf TSpm levels compared with the controls. Accordantly, overexpression of CsACL5 in cucumber plants markedly increased leaf TSpm levels and enhanced defense against B. cinerea infection. The functions of TSpm catabolism in the DN16-mediated defense responses of cucumber plants to B. cinerea were further investigated by pharmacological approaches. Upon exposure to pathogen infection, the changes of leaf TSpm levels were positively related to the enhanced activities of polyamine catabolic enzymes including polyamine oxidases (PAOs) and copper amine oxidases (CuAOs), which paralleled the transcription of several defense-related genes such as pathogenesis-related protein 1 (CsPR1) and defensin-like protein 1 (CsDLP1). However, the inhibited activities of polyamine catabolic enzymes abolished the DN16-induced cucumber defense against B. cinerea infection. This was in line with the impaired expression of defense-related genes in the inoculated plants challenged by B. cinerea. Collectively, our findings unraveled a pivotal role of TSpm catabolism in the regulation of the rhizobacteria-primed defense states by mediating the immune responses in cucumber plants after B. cinerea infection.


2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Wen-Tien Wu ◽  
Yi-Ru Chen ◽  
Dai-Hua Lu ◽  
Fedor Svyatoslavovich Senatov ◽  
Kai-Chiang Yang ◽  
...  

Abstract Background Silymarin (SMN), a polyphenolic flavonoid, is involved in multiple bioactive functions including anti-inflammation. Pretreatment with SMN demonstrated chondroprotection against tumour necrosis factor-alpha (TNF-α) stimulation in a chondrocyte cell line. However, pre- and posttreatment with phytochemicals have varying effects on osteoarthritis (OA) chondrocytes, and the therapeutic potential of SMN after catabolic cytokine stimulation is not fully elucidated. Methods The cytotoxicity of SMN (12.5, 25, 50 and 100 μM) was evaluated in human primary chondrocytes. The chondrocytes were supplemented with SMN (25 and 50 μM) after interleukin-1beta (IL-1β) stimulation. The mRNA expression and protein production of catabolic/anabolic cytokines as well as extracellular matrix (ECM) components were evaluated. Results High-dose SMN (100 μM) impaired the mitochondrial activity in chondrocytes, and 50 μM SMN further caused cell death in IL-1β-stimulated cells. The addition of 25 μM SMN ameliorated cell senescence; downregulated the catabolic genes of inducible nitric oxide synthase, IL-1β, TNF-α, matrix metalloproteinase-3 (MMP-3), MMP-9 and MMP-13; upregulated the anabolic genes of tissue inhibitor of metalloproteinase-1 (TIMP-1) and collagen type II alpha 1; and restored the expression of chondrogenic phenotype genes SOX9 and sirtuin-1 (Sirt1). In addition, the production of IL-1β, MMP-3 and MMP-9 decreased with an increase in TIMP-1 secretion. However, the mRNA levels of IL-6, IL-8 and IL-10 and protein production remained high. The addition of nicotinamide, a Sirt1 inhibitor, downregulated SOX9 and attenuated the therapeutic effects of SMN on IL-1β-stimulated chondrocytes. Conclusion SMN regulates the chondrocyte phenotype through Sirt1 and SOX9 to improve ECM homeostasis and may serve as a complementary therapy for early-stage knee OA.


Author(s):  
Sandhya Mishra ◽  
Ziqiu Lin ◽  
Shimei Pang ◽  
Wenping Zhang ◽  
Pankaj Bhatt ◽  
...  

Global environmental contamination with a complex mixture of xenobiotics has become a major environmental issue worldwide. Many xenobiotic compounds severely impact the environment due to their high toxicity, prolonged persistence, and limited biodegradability. Microbial-assisted degradation of xenobiotic compounds is considered to be the most effective and beneficial approach. Microorganisms have remarkable catabolic potential, with genes, enzymes, and degradation pathways implicated in the process of biodegradation. A number of microbes, including Alcaligenes, Cellulosimicrobium, Microbacterium, Micrococcus, Methanospirillum, Aeromonas, Sphingobium, Flavobacterium, Rhodococcus, Aspergillus, Penecillium, Trichoderma, Streptomyces, Rhodotorula, Candida, and Aureobasidium, have been isolated and characterized, and have shown exceptional biodegradation potential for a variety of xenobiotic contaminants from soil/water environments. Microorganisms potentially utilize xenobiotic contaminants as carbon or nitrogen sources to sustain their growth and metabolic activities. Diverse microbial populations survive in harsh contaminated environments, exhibiting a significant biodegradation potential to degrade and transform pollutants. However, the study of such microbial populations requires a more advanced and multifaceted approach. Currently, multiple advanced approaches, including metagenomics, proteomics, transcriptomics, and metabolomics, are successfully employed for the characterization of pollutant-degrading microorganisms, their metabolic machinery, novel proteins, and catabolic genes involved in the degradation process. These technologies are highly sophisticated, and efficient for obtaining information about the genetic diversity and community structures of microorganisms. Advanced molecular technologies used for the characterization of complex microbial communities give an in-depth understanding of their structural and functional aspects, and help to resolve issues related to the biodegradation potential of microorganisms. This review article discusses the biodegradation potential of microorganisms and provides insights into recent advances and omics approaches employed for the specific characterization of xenobiotic-degrading microorganisms from contaminated environments.


Biomolecules ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 245
Author(s):  
Morgane Bourmaud ◽  
Mylene Zarka ◽  
Romain Le Cozannet ◽  
Pascale Fança-Berthon ◽  
Eric Hay ◽  
...  

Osteoarthritis is characterized by cartilage loss resulting from the activation of chondrocytes associated with a synovial inflammation. Activated chondrocytes promote an increased secretion of matrix proteases and proinflammatory cytokines leading to cartilage breakdown. Since natural products possess anti-inflammatory properties, we investigated the direct effect of Rubus idaeus extracts (RIE) in chondrocyte metabolism and cartilage loss. The effect of RIE in chondrocyte metabolism was analyzed in murine primary chondrocytes and cartilage explants. We also assessed the contribution of RIE in an inflammation environment by culturing mice primary chondrocytes with the supernatant of Raw 264.7 macrophage-like cells primed with RIE. In primary chondrocytes, RIE diminished chondrocyte hypertrophy (Col10), while increasing the expression of catabolic genes (Mmp-3, Mmp-13) and reducing anabolic genes (Col2a1, Acan). In cartilage explants, Rubus idaeus prevented the loss of proteoglycan (14.84 ± 3.07% loss of proteoglycans with IL1 alone vs. 3.03 ± 1.86% with IL1 and 100 µg/mL of RIE), as well as the NITEGE neoepitope expression. RIE alone reduced the expression of Il1 and Il6 in macrophages, without changes in Tnf and Cox2 expression. The secretome of macrophages pre-treated with RIE and transferred to chondrocytes decreases the gene and protein expression of Mmp-3 and Cox2. In conclusion, these data suggest that RIE may protect from chondrocyte catabolism and cartilage loss in inflammatory conditions. Further evaluations are need before considering RIE as a candidate for the treatment for osteoarthritis.


AMB Express ◽  
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Matthew Chekwube Enebe ◽  
Olubukola Oluranti Babalola

AbstractSoil microbes perform important functions in nitrogen and carbon cycling in the biosphere. Microbial communities in the rhizosphere enhance plants’ health and promote nutrient turnover and cycling in the soil. In this study, we evaluated the effects of soil fertilization with organic and inorganic fertilizers on the abundances and distribution of carbon and nitrogen cycling genes within the rhizosphere of maize plants. Our result showed that maize plants through rhizosphere effects selected and enriched the same functional genes glnA, gltB, gudB involved in nitrogen cycle as do high compost and low inorganic fertilizer treatments. This observation was significantly different from those of high doses of inorganic fertilizer and low compost manure treated soil. Only alpha amylase encoding genes were selectively enriched by low compost and high inorganic fertilized soil. The other treatments only selected xynB (in Cp8), lacZ (Cp4), bglA, pldB, trpA (N2), uidA (N1) and glgC, vanA (Cn0) carbon cycling genes in the rhizosphere of maize. Also Actinomycetales are selected by high compost, low inorganic fertilizer and control. The control was without any fertilization and the soil was planted with maize. Bacillales are also promoted by low compost and high inorganic fertilizer. This indicated that only microbes capable of tolerating the stress of high dose of inorganic fertilizer will thrive under such condition. Therefore, soil fertilization lowers nitrogen gas emission as seen with the high abundance of nitrogen assimilation genes or microbial anabolic genes, but increases carbon dioxide evolution in the agricultural soil by promoting the abundance of catabolic genes involve in carbon cycling.


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