The Identification and Cloning of Genes Encoding Haloaromatic Catabolic Enzymes and the Construction of Hybrid Pathways for Substrate Mineralization

1984 ◽  
pp. 47-80 ◽  
Author(s):  
A. J. Weightman ◽  
R. H. Don ◽  
P. R. Lehrbach ◽  
K. N. Timmis
Keyword(s):  
Catabolic Enzymes ◽  
Genes Encoding

scholarly journals Transcriptomic Assessment of Isozymes in the Biphenyl Pathway of Rhodococcus sp. Strain RHA1

2006 ◽  
Vol 72 (9) ◽  
pp. 6183-6193 ◽  
Author(s):  
Edmilson R. Gon�alves ◽  
Hirofumi Hara ◽  
Daisuke Miyazawa ◽  
Julian E. Davies ◽  
Lindsay D. Eltis ◽  
...  
Keyword(s):  
Dna Microarray ◽  
Aromatic Compounds ◽  
Regulatory Mechanism ◽  
Sequence Analyses ◽  
Catabolic Enzymes ◽  
Catabolic Genes ◽  
Genes Encoding ◽  
Pcr Assays ◽  
Alkyl Benzenes ◽  
Rhodococcus Sp

ABSTRACT Rhodococcus sp. RHA1 grows on a broad range of aromatic compounds and vigorously degrades polychlorinated biphenyls (PCBs). Previous work identified RHA1 genes encoding multiple isozymes for most of the seven steps of the biphenyl (BPH) pathway, provided evidence for coexpression of some of these isozymes, and indicated the involvement of some of these enzymes in the degradation of BPH, ethylbenzene (ETB), and PCBs. To investigate the expression of these isozymes and better understand how they contribute to the robust degradative capacity of RHA1, we comprehensively analyzed the 9.7-Mb genome of RHA1 for BPH pathway genes and characterized the transcriptome of RHA1 growing on benzoate (BEN), BPH, and ETB. Sequence analyses revealed 54 potential BPH pathway genes, including 28 not previously reported. Transcriptomic analysis with a DNA microarray containing 70-mer probes for 8,213 RHA1 genes revealed a suite of 320 genes of diverse functions that were upregulated during growth both on BPH and on ETB, relative to growth on the control substrate, pyruvate. By contrast, only 65 genes were upregulated during growth on BEN. Quantitative PCR assays confirmed microarray results for selected genes and indicated that some of the catabolic genes were upregulated over 10,000-fold. Our analysis suggests that up to 22 enzymes, including 8 newly identified ones, may function in the BPH pathway of RHA1. The relative expression levels of catabolic genes did not differ for BPH and ETB, suggesting a common regulatory mechanism. This study delineated a suite of catabolic enzymes for biphenyl and alkyl-benzenes in RHA1, which is larger than previously recognized and which may serve as a model for catabolism in other environmentally important bacteria having large genomes.

scholarly journals Genetic Engineering of Zymobacter palmae for Production of Ethanol from Xylose

2007 ◽  
Vol 73 (8) ◽  
pp. 2592-2599 ◽  
Author(s):  
Hideshi Yanase ◽  
Dai Sato ◽  
Keiko Yamamoto ◽  
Saori Matsuda ◽  
Sho Yamamoto ◽  
...  
Keyword(s):  
Xylose Isomerase ◽  
Metabolic Characteristics ◽  
Catabolic Enzymes ◽  
Theoretical Yield ◽  
Genetic Modifications ◽  
Xylose Uptake ◽  
Genes Encoding ◽  
Pentose Sugar ◽  
Efficient Fermentation ◽  
Zymobacter Palmae

ABSTRACT Its metabolic characteristics suggest that Zymobacter palmae gen. nov., sp. nov. could serve as a useful new ethanol-fermenting bacterium, but its biotechnological exploitation will require certain genetic modifications. We therefore engineered Z. palmae so as to broaden the range of its fermentable sugar substrates to include the pentose sugar xylose. The Escherichia coli genes encoding the xylose catabolic enzymes xylose isomerase, xylulokinase, transaldolase, and transketolase were introduced into Z. palmae, where their expression was driven by the Zymomonas mobilis glyceraldehyde-3-phosphate dehydrogenase promoter. When cultured with 40 g/liter xylose, the recombinant Z. palmae strain was able to ferment 16.4 g/liter xylose within 5 days, producing 91% of the theoretical yield of ethanol with no accumulation of organic acids as metabolic by-products. Notably, xylose acclimation enhanced both the expression of xylose catabolic enzymes and the rate of xylose uptake into recombinant Z. palmae, which enabled the acclimated organism to completely and simultaneously ferment a mixture of 40 g/liter glucose and 40 g/liter xylose within 8 h, producing 95% of the theoretical yield of ethanol. Thus, efficient fermentation of a mixture of glucose and xylose to ethanol can be accomplished by using Z. palmae expressing E. coli xylose catabolic enzymes.

scholarly journals Mechanistic insights into the success of xenobiotic degraders resolved from metagenomes of microbial enrichment cultures

2021 ◽  
Author(s):  
Junhui Li ◽  
Chongjian Jia ◽  
Qihong Lu ◽  
Bruce A Hungate ◽  
Paul Dijkstra ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Contaminated Soils ◽  
Microbial Processes ◽  
Positive Interactions ◽  
Ecological Strategies ◽  
Catabolic Enzymes ◽  
Catabolic Genes ◽  
Genes Encoding ◽  
Micro Organisms ◽  
Xenobiotic Biodegradation

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.

DNA methylation in satellite repeats disorders

2019 ◽  
Vol 63 (6) ◽  
pp. 757-771 ◽  
Author(s):  
Claire Francastel ◽  
Frédérique Magdinier
Keyword(s):  
Dna Methylation ◽  
Human Genome ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Satellite Repeats ◽  
Tremendous Progress ◽  
Genes Encoding ◽  
Dna Elements ◽  
Near Future

Abstract Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.

Sign in / Sign up

Export Citation Format

Share Document