Special Issue "Genetics of Biodegradation and Bioremediation"

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: closed (31 March 2019).

Special Issue Editors

Guest Editor
Prof. Eduardo Santero Website E-Mail
Departamento de Biologia Molecular e Ingenieria Bioquimica, Centro Andaluz de Biologia del Desarrollo, Universidad Pablo de Olavide, Ctra. Utrera Km 1, 41013-Sevilla, Spain
Phone: 954349386 (office) 9053 (lab).
Fax: 954349376
Interests: biodegradation organic contaminants; catabolic pathways characterization; gene expression regulation in bacteria; nitrogen metabolism control; carbon catabolite repression; design of expression systems in bacteria
Guest Editor
Prof. Eduardo Díaz Website E-Mail
Microbial and Plant Biotechnology Departament, Biological Research Centre (CIB)-CSIC, Madrid, Spain
Interests: Anaerobic degradation; Transcriptional regulation; Metabolic engineering; Regulatory circuits; Gene transfer

Special Issue Information

Dear Colleagues,

Industrial activity has resulted in the production of huge amounts of compounds, many of them xenobiotics, which are very persistent in nature because of their stable chemical structure, low biodegradability, or toxicity, and accumulate to concentrations that affect the environment. However, several bacteria have evolved to metabolize these contaminants, in many cases using them as nutrient or energy sources.

Many different biodegradation pathways have already been characterised, and the phylogenetic relationships among biodegradation genes within the different types of pathways have been studied. However, new biodegrading activities and their coding genes are continuously being reported, including those involved in the biodegradation of emerging contaminants or those generally regarded as non-biodegradable. New biodegradation pathways can be assembled in a strain or a bacterial consortium by recruiting biodegradation genes from different origins through horizontal gene transfer. Gene regulation is also an important issue for the efficient biodegradation of contaminants. Specific induction by the substrate and over-imposed global regulatory networks adjust the expression of the biodegradation genes to the bacterial physiological needs. The abundance and diversity of biodegradation genes, analysed by either genomic or metagenomic approaches, is an indicator of the biodegradation potential of a niche and is used together with contaminant biosensors to follow the progress of natural or programmed bioremediation programs.

This Special issue will cover the genetic, genomic or metagenomic identification and characterisation of biodegradation genes, gene products and their host strains, as long as gene regulation, transport, monitoring in the environment or utilisation of biodegradation genes or their regulatory systems as reporters, biosensors or expression platforms, either in oxic, anoxic or extreme environments. We cordially invite researchers working in these areas to contribute with original research or review papers.

Prof. Eduardo Santero
Prof. Eduardo Díaz
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Biodegradation
  • Bioremediation
  • Catabolic pathway
  • Mobile DNA
  • Anaerobic biodegradation
  • Gene regulation
  • Transport
  • Regulatory circuits
  • Biomonitoring

Published Papers (11 papers)

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Research

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Open AccessArticle
Genomic Analysis of γ-Hexachlorocyclohexane-Degrading Sphingopyxis lindanitolerans WS5A3p Strain in the Context of the Pangenome of Sphingopyxis
Genes 2019, 10(9), 688; https://doi.org/10.3390/genes10090688 - 06 Sep 2019
Abstract
Sphingopyxis inhabit diverse environmental niches, including marine, freshwater, oceans, soil and anthropogenic sites. The genus includes 20 phylogenetically distinct, valid species, but only a few with a sequenced genome. In this work, we analyzed the nearly complete genome of the newly described species, [...] Read more.
Sphingopyxis inhabit diverse environmental niches, including marine, freshwater, oceans, soil and anthropogenic sites. The genus includes 20 phylogenetically distinct, valid species, but only a few with a sequenced genome. In this work, we analyzed the nearly complete genome of the newly described species, Sphingopyxis lindanitolerans, and compared it to the other available Sphingopyxis genomes. The genome included 4.3 Mbp in total and consists of a circular chromosome, and two putative plasmids. Among the identified set of lin genes responsible for γ-hexachlorocyclohexane pesticide degradation, we discovered a gene coding for a new isoform of the LinA protein. The significant potential of this species in the remediation of contaminated soil is also correlated with the fact that its genome encodes a higher number of enzymes potentially involved in aromatic compound degradation than for most other Sphingopyxis strains. Additional analysis of 44 Sphingopyxis representatives provides insights into the pangenome of Sphingopyxis and revealed a core of 734 protein clusters and between four and 1667 unique proteins per genome. Full article
(This article belongs to the Special Issue Genetics of Biodegradation and Bioremediation)
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Open AccessArticle
A Case of Adaptive Laboratory Evolution (ALE): Biodegradation of Furfural by Pseudomonas pseudoalcaligenes CECT 5344
Genes 2019, 10(7), 499; https://doi.org/10.3390/genes10070499 - 29 Jun 2019
Abstract
Pseudomonas pseudoalcaligenes CECT 5344 is a bacterium able to assimilate cyanide as a nitrogen source at alkaline pH. Genome sequencing of this strain allowed the detection of genes related to the utilization of furfurals as a carbon and energy source. Furfural and 5-(hydroxymethyl) [...] Read more.
Pseudomonas pseudoalcaligenes CECT 5344 is a bacterium able to assimilate cyanide as a nitrogen source at alkaline pH. Genome sequencing of this strain allowed the detection of genes related to the utilization of furfurals as a carbon and energy source. Furfural and 5-(hydroxymethyl) furfural (HMF) are byproducts of sugars production during the hydrolysis of lignocellulosic biomass. Since they inhibit the yeast fermentation to obtain bioethanol from sugars, the biodegradation of these compounds has attracted certain scientific interest. P. pseudoalcaligenes was able to use furfuryl alcohol, furfural and furoic acid as carbon sources, but after a lag period of several days. Once adapted, the evolved strain (R1D) did not show any more prolonged lag phases. The transcriptomic analysis (RNA-seq) of R1D revealed a non-conservative punctual mutation (L261R) in BN5_2307, a member of the AraC family of activators, modifying the charge of the HTH region of the protein. The inactivation of the mutated gene in the evolved strain by double recombination reverted to the original phenotype. Although the bacterium did not assimilate HMF, it transformed it into value-added building blocks for the chemical industry. These results could be used to improve the production of cost-effective second-generation biofuels from agricultural wastes. Full article
(This article belongs to the Special Issue Genetics of Biodegradation and Bioremediation)
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Open AccessArticle
Further Insights into the Architecture of the PN Promoter That Controls the Expression of the bzd Genes in Azoarcus
Genes 2019, 10(7), 489; https://doi.org/10.3390/genes10070489 - 27 Jun 2019
Abstract
The anaerobic degradation of benzoate in bacteria involves the benzoyl-CoA central pathway. Azoarcus/Aromatoleum strains are a major group of anaerobic benzoate degraders, and the transcriptional regulation of the bzd genes was extensively studied in Azoarcus sp. CIB. In this work, we [...] Read more.
The anaerobic degradation of benzoate in bacteria involves the benzoyl-CoA central pathway. Azoarcus/Aromatoleum strains are a major group of anaerobic benzoate degraders, and the transcriptional regulation of the bzd genes was extensively studied in Azoarcus sp. CIB. In this work, we show that the bzdR regulatory gene and the PN promoter can also be identified upstream of the catabolic bzd operon in all benzoate-degrader Azoarcus/Aromatoleum strains whose genome sequences are currently available. All the PN promoters from Azoarcus/Aromatoleum strains described here show a conserved architecture including three operator regions (ORs), i.e., OR1 to OR3, for binding to the BzdR transcriptional repressor. Here, we demonstrate that, whereas OR1 is sufficient for the BzdR-mediated repression of the PN promoter, the presence of OR2 and OR3 is required for de-repression promoted by the benzoyl-CoA inducer molecule. Our results reveal that BzdR binds to the PN promoter in the form of four dimers, two of them binding to OR1. The BzdR/PN complex formed induces a DNA loop that wraps around the BzdR dimers and generates a superstructure that was observed by atomic force microscopy. This work provides further insights into the existence of a conserved BzdR-dependent mechanism to control the expression of the bzd genes in Azoarcus strains. Full article
(This article belongs to the Special Issue Genetics of Biodegradation and Bioremediation)
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Open AccessArticle
Metagenomic Insights into the Bacterial Functions of a Diesel-Degrading Consortium for the Rhizoremediation of Diesel-Polluted Soil
Genes 2019, 10(6), 456; https://doi.org/10.3390/genes10060456 - 14 Jun 2019
Abstract
Diesel is a complex pollutant composed of a mixture of aliphatic and aromatic hydrocarbons. Because of this complexity, diesel bioremediation requires multiple microorganisms, which harbor the catabolic pathways to degrade the mixture. By enrichment cultivation of rhizospheric soil from a diesel-polluted site, we [...] Read more.
Diesel is a complex pollutant composed of a mixture of aliphatic and aromatic hydrocarbons. Because of this complexity, diesel bioremediation requires multiple microorganisms, which harbor the catabolic pathways to degrade the mixture. By enrichment cultivation of rhizospheric soil from a diesel-polluted site, we have isolated a bacterial consortium that can grow aerobically with diesel and different alkanes and polycyclic aromatic hydrocarbons (PAHs) as the sole carbon and energy source. Microbiome diversity analyses based on 16S rRNA gene showed that the diesel-degrading consortium consists of 76 amplicon sequence variants (ASVs) and it is dominated by Pseudomonas, Aquabacterium, Chryseobacterium, and Sphingomonadaceae. Changes in microbiome composition were observed when growing on specific hydrocarbons, reflecting that different populations degrade different hydrocarbons. Shotgun metagenome sequence analysis of the consortium growing on diesel has identified redundant genes encoding enzymes implicated in the initial oxidation of alkanes (AlkB, LadA, CYP450) and a variety of hydroxylating and ring-cleavage dioxygenases involved in aromatic and polyaromatic hydrocarbon degradation. The phylogenetic assignment of these enzymes to specific genera allowed us to model the role of specific populations in the diesel-degrading consortium. Rhizoremediation of diesel-polluted soil microcosms using the consortium, resulted in an important enhancement in the reduction of total petroleum hydrocarbons (TPHs), making it suited for rhizoremediation applications. Full article
(This article belongs to the Special Issue Genetics of Biodegradation and Bioremediation)
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Open AccessArticle
Genomic Diversity of Two Hydrocarbon-Degrading and Plant Growth-Promoting Pseudomonas Species Isolated from the Oil Field of Bóbrka (Poland)
Genes 2019, 10(6), 443; https://doi.org/10.3390/genes10060443 - 11 Jun 2019
Abstract
Hydrocarbon-degrading bacteria are important resources for use in phytoremediation applications. Yet, for many hydrocarbonoclastic strains the genetic information regarding pollutant degradation and detoxification has not been thoroughly revealed. In this study, hydrocarbon-degrading bacteria were isolated from a long-term oil-polluted soil in Bóbrka, Poland. [...] Read more.
Hydrocarbon-degrading bacteria are important resources for use in phytoremediation applications. Yet, for many hydrocarbonoclastic strains the genetic information regarding pollutant degradation and detoxification has not been thoroughly revealed. In this study, hydrocarbon-degrading bacteria were isolated from a long-term oil-polluted soil in Bóbrka, Poland. Pseudomonas spp. was the most dominant species. Of all 69 isolated strains tested in the laboratory using qualitative biochemical assays, 61% showed the capability to use diesel as sole carbon source, 33% could produce indole, 19% produced siderophores, 36% produced organic acids, and 54% were capable of producing 1-aminocyclopropane-1-carboxylate (ACC)-deaminase. From all morphologically and genetically different strains, two representative Pseudomonas spp., strain VI4.1 and VI4T1, were selected for genome sequencing. Genomic analyses indicated the presence of the full naphthalene dioxygenase operon (plasmid and chromosomal), of genes involved in the degradation of BTEX compounds (Benzene, Toluene, Ethylbenzene, Xylene) and alkanes (alkB gene) as well as the anthranilate degradation pathway (strain VI4T1) and terephthalate dioxygenase protein (strain VI4.1). Proton transfer reaction time-of-flight mass spectrometry (PTR-TOF-MS) analyses confirmed naphthalene and BTEX degradation within seven days. Motility, resistance to abiotic stresses, high and low temperatures, low pH, and salinity were confirmed at the genetic level and experimentally verified. The presence of multiple degradative and plant growth promotion genes, together with the in vitro experimental evidence, indicates the high value of these two strains and their potential use for sustainable site clean-up. Full article
(This article belongs to the Special Issue Genetics of Biodegradation and Bioremediation)
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Open AccessArticle
Engineering CatM, a LysR-Type Transcriptional Regulator, to Respond Synergistically to Two Effectors
Genes 2019, 10(6), 421; https://doi.org/10.3390/genes10060421 - 31 May 2019
Abstract
The simultaneous response of one transcriptional regulator to different effectors remains largely unexplored. Nevertheless, such interactions can substantially impact gene expression by rapidly integrating cellular signals and by expanding the range of transcriptional responses. In this study, similarities between paralogs were exploited to [...] Read more.
The simultaneous response of one transcriptional regulator to different effectors remains largely unexplored. Nevertheless, such interactions can substantially impact gene expression by rapidly integrating cellular signals and by expanding the range of transcriptional responses. In this study, similarities between paralogs were exploited to engineer novel responses in CatM, a regulator that controls benzoate degradation in Acinetobacter baylyi ADP1. One goal was to improve understanding of how its paralog, BenM, activates transcription in response to two compounds (cis,cis-muconate and benzoate) at levels significantly greater than with either alone. Despite the overlapping functions of BenM and CatM, which regulate many of the same ben and cat genes, CatM normally responds only to cis,cis-muconate. Using domain swapping and site-directed amino acid replacements, CatM variants were generated and assessed for the ability to activate transcription. To create a variant that responds synergistically to both effectors required alteration of both the effector-binding region and the DNA-binding domain. These studies help define the interconnected roles of protein domains and extend understanding of LysR-type proteins, the largest family of transcriptional regulators in bacteria. Additionally, renewed interest in the modular functionality of transcription factors stems from their potential use as biosensors. Full article
(This article belongs to the Special Issue Genetics of Biodegradation and Bioremediation)
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Open AccessArticle
Biphenyl/PCB Degrading bph Genes of Ten Bacterial Strains Isolated from Biphenyl-Contaminated Soil in Kitakyushu, Japan: Comparative and Dynamic Features as Integrative Conjugative Elements (ICEs)
Genes 2019, 10(5), 404; https://doi.org/10.3390/genes10050404 - 27 May 2019
Abstract
We sequenced the entire genomes of ten biphenyl/PCB degrading bacterial strains (KF strains) isolated from biphenyl-contaminated soil in Kitakyushu, Japan. All the strains were Gram-negative bacteria belonging to β- and γ-proteobacteria. Out of the ten strains, nine strains carried a biphenyl catabolic bph [...] Read more.
We sequenced the entire genomes of ten biphenyl/PCB degrading bacterial strains (KF strains) isolated from biphenyl-contaminated soil in Kitakyushu, Japan. All the strains were Gram-negative bacteria belonging to β- and γ-proteobacteria. Out of the ten strains, nine strains carried a biphenyl catabolic bph gene cluster as integrative conjugative elements (ICEs), and they were classified into four groups based on the structural features of the bph genes. Group I (five strains) possessed bph genes that were very similar to the ones in Pseudomonas furukawaii KF707 (formerly Pseudomonas pseudoalcaligenes KF707), which is one of the best characterized biphenyl-utilizing strains. This group of strains carried salicylate catabolic sal genes that were approximately 6-kb downstream of the bph genes. Group II (two strains) possessed bph and sal genes similar to the ones in KF707, but these strains lacked the bphX region between bphC and bphD, which is involved in the downstream catabolism of biphenyl. These bph-sal clusters in groups I and II were located on an integrative conjugative element that was larger than 110 kb, and they were named ICEbph-sal. Our previous study demonstrated that the ICEbph-sal of Pseudomonas putida KF715 in group II existed both in an integrated form in the chromosome (referred to as ICEbph-salKF715 (integrated)) and in a extrachromosomal circular form (referred to as ICEbph-sal (circular)) (previously called pKF715A, 483 kb) in the stationary culture. The ICEbph-sal was transferred from KF715 into P. putida AC30 and P. putida KT2440 with high frequency, and it was maintained stably as an extrachromosomal circular form. The ICEbph-salKF715 (circular) in these transconjugants was further transferred to P. putida F39/D and then integrated into the chromosome in one or two copies. Meanwhile, group III (one strain) possessed bph genes, but not sal genes. The nucleotide sequences of the bph genes in this group were less conserved compared to the genes of the strains belonging to groups I and II. Currently, there is no evidence to indicate that the bph genes in group III are carried by a mobile element. Group IV (two strains) carried bph genes as ICEs (59–61 kb) that were similar to the genes found in Tn4371 from Cupriavidus oxalacticus A5 and ICEKKS1024677 from the Acidovorax sp. strain KKS102. Our study found that bph gene islands have integrative functions, are transferred among soil bacteria, and are diversified through modification. Full article
(This article belongs to the Special Issue Genetics of Biodegradation and Bioremediation)
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Review

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Open AccessReview
Variability in Assembly of Degradation Operons for Naphthalene and its derivative, Carbaryl, Suggests Mobilization through Horizontal Gene Transfer
Genes 2019, 10(8), 569; https://doi.org/10.3390/genes10080569 - 27 Jul 2019
Abstract
In the biosphere, the largest biological laboratory, increased anthropogenic activities have led microbes to evolve and adapt to the changes occurring in the environment. Compounds, specifically xenobiotics, released due to such activities persist in nature and undergo bio-magnification in the food web. Some [...] Read more.
In the biosphere, the largest biological laboratory, increased anthropogenic activities have led microbes to evolve and adapt to the changes occurring in the environment. Compounds, specifically xenobiotics, released due to such activities persist in nature and undergo bio-magnification in the food web. Some of these compounds act as potent endocrine disrupters, mutagens or carcinogens, and therefore their removal from the environment is essential. Due to their persistence, microbial communities have evolved to metabolize them partially or completely. Diverse biochemical pathways have evolved or been assembled by exchange of genetic material (horizontal gene transfer) through various mobile genetic elements like conjugative and non-conjugative plasmids, transposons, phages and prophages, genomic islands and integrative conjugative elements. These elements provide an unlimited opportunity for genetic material to be exchanged across various genera, thus accelerating the evolution of a new xenobiotic degrading phenotype. In this article, we illustrate examples of the assembly of metabolic pathways involved in the degradation of naphthalene and its derivative, Carbaryl, which are speculated to have evolved or adapted through the above-mentioned processes. Full article
(This article belongs to the Special Issue Genetics of Biodegradation and Bioremediation)
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Open AccessReview
Steroids as Environmental Compounds Recalcitrant to Degradation: Genetic Mechanisms of Bacterial Biodegradation Pathways
Genes 2019, 10(7), 512; https://doi.org/10.3390/genes10070512 - 06 Jul 2019
Abstract
Steroids are perhydro-1,2-cyclopentanophenanthrene derivatives that are almost exclusively synthesised by eukaryotic organisms. Since the start of the Anthropocene, the presence of these molecules, as well as related synthetic compounds (ethinylestradiol, dexamethasone, and others), has increased in different habitats due to farm and municipal [...] Read more.
Steroids are perhydro-1,2-cyclopentanophenanthrene derivatives that are almost exclusively synthesised by eukaryotic organisms. Since the start of the Anthropocene, the presence of these molecules, as well as related synthetic compounds (ethinylestradiol, dexamethasone, and others), has increased in different habitats due to farm and municipal effluents and discharge from the pharmaceutical industry. In addition, the highly hydrophobic nature of these molecules, as well as the absence of functional groups, makes them highly resistant to biodegradation. However, some environmental bacteria are able to modify or mineralise these compounds. Although steroid-metabolising bacteria have been isolated since the beginning of the 20th century, the genetics and catabolic pathways used have only been characterised in model organisms in the last few decades. Here, the metabolic alternatives used by different bacteria to metabolise steroids (e.g., cholesterol, bile acids, testosterone, and other steroid hormones), as well as the organisation and conservation of the genes involved, are reviewed. Full article
(This article belongs to the Special Issue Genetics of Biodegradation and Bioremediation)
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Open AccessReview
Microbial Genes for a Circular and Sustainable Bio-PET Economy
Genes 2019, 10(5), 373; https://doi.org/10.3390/genes10050373 - 16 May 2019
Abstract
Plastics have become an important environmental concern due to their durability and resistance to degradation. Out of all plastic materials, polyesters such as polyethylene terephthalate (PET) are amenable to biological degradation due to the action of microbial polyester hydrolases. The hydrolysis products obtained [...] Read more.
Plastics have become an important environmental concern due to their durability and resistance to degradation. Out of all plastic materials, polyesters such as polyethylene terephthalate (PET) are amenable to biological degradation due to the action of microbial polyester hydrolases. The hydrolysis products obtained from PET can thereby be used for the synthesis of novel PET as well as become a potential carbon source for microorganisms. In addition, microorganisms and biomass can be used for the synthesis of the constituent monomers of PET from renewable sources. The combination of both biodegradation and biosynthesis would enable a completely circular bio-PET economy beyond the conventional recycling processes. Circular strategies like this could contribute to significantly decreasing the environmental impact of our dependence on this polymer. Here we review the efforts made towards turning PET into a viable feedstock for microbial transformations. We highlight current bottlenecks in degradation of the polymer and metabolism of the monomers, and we showcase fully biological or semisynthetic processes leading to the synthesis of PET from sustainable substrates. Full article
(This article belongs to the Special Issue Genetics of Biodegradation and Bioremediation)
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Open AccessReview
Biodegradation of Tetralin: Genomics, Gene Function and Regulation
Genes 2019, 10(5), 339; https://doi.org/10.3390/genes10050339 - 06 May 2019
Abstract
Tetralin (1,2,3,4-tetrahydonaphthalene) is a recalcitrant compound that consists of an aromatic and an alicyclic ring. It is found in crude oils, produced industrially from naphthalene or anthracene, and widely used as an organic solvent. Its toxicity is due to the alteration of biological [...] Read more.
Tetralin (1,2,3,4-tetrahydonaphthalene) is a recalcitrant compound that consists of an aromatic and an alicyclic ring. It is found in crude oils, produced industrially from naphthalene or anthracene, and widely used as an organic solvent. Its toxicity is due to the alteration of biological membranes by its hydrophobic character and to the formation of toxic hydroperoxides. Two unrelated bacteria, Sphingopyxis granuli strain TFA and Rhodococcus sp. strain TFB were isolated from the same niche as able to grow on tetralin as the sole source of carbon and energy. In this review, we provide an overview of current knowledge on tetralin catabolism at biochemical, genetic and regulatory levels in both strains. Although they share the same biodegradation strategy and enzymatic activities, no evidences of horizontal gene transfer between both bacteria have been found. Moreover, the regulatory elements that control the expression of the gene clusters are completely different in each strain. A special consideration is given to the complex regulation discovered in TFA since three regulatory systems, one of them involving an unprecedented communication between the catabolic pathway and the regulatory elements, act together at transcriptional and posttranscriptional levels to optimize tetralin biodegradation gene expression to the environmental conditions. Full article
(This article belongs to the Special Issue Genetics of Biodegradation and Bioremediation)
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