Streit WR

References (35)

Title : New dienelactone hydrolase from microalgae bacterial community-Antibiofilm activity against fish pathogens and potential applications for aquaculture - Bergmann_2024_Sci.Rep_14_377
Author(s) : Bergmann L , Balzer Le S , Hageskal G , Preuss L , Han Y , Astafyeva Y , Loevenich S , Emmann S , Perez-Garcia P , Indenbirken D , Katzowitsch E , Thummler F , Alawi M , Wentzel A , Streit WR , Krohn I
Ref : Sci Rep , 14 :377 , 2024
Abstract : Biofilms are resistant to many traditional antibiotics, which has led to search for new antimicrobials from different and unique sources. To harness the potential of aquatic microbial resources, we analyzed the meta-omics datasets of microalgae-bacteria communities and mined them for potential antimicrobial and quorum quenching enzymes. One of the most interesting candidates (Dlh3), a dienelactone hydrolase, is a alpha/beta-protein with predicted eight alpha-helices and eight beta-sheets. When it was applied to one of the major fish pathogens, Edwardsiella anguillarum, the biofilm development was reproducibly inhibited by up to 54.5%. The transcriptome dataset in presence of Dlh3 showed an upregulation in functions related to self-defense like active genes for export mechanisms and transport systems. The most interesting point regarding the biotechnological potential for aquaculture applications of Dlh3 are clear evidence of biofilm inhibition and that health and division of a relevant fish cell model (CHSE-214) was not impaired by the enzyme.
ESTHER : Bergmann_2024_Sci.Rep_14_377
PubMedSearch : Bergmann_2024_Sci.Rep_14_377
PubMedID: 38172513
Gene_locus related to this paper: 9sphn-ErcDlh3

Title : An archaeal lid-containing feruloyl esterase degrades polyethylene terephthalate - Perez-Garcia_2023_Commun.Chem_6_193
Author(s) : Perez-Garcia P , Chow J , Costanzi E , Gurschke M , Dittrich J , Dierkes RF , Molitor R , Applegate V , Feuerriegel G , Tete P , Danso D , Thies S , Schumacher J , Pfleger C , Jaeger KE , Gohlke H , Smits SHJ , Schmitz RA , Streit WR
Ref : Commun Chem , 6 :193 , 2023
Abstract : Polyethylene terephthalate (PET) is a commodity polymer known to globally contaminate marine and terrestrial environments. Today, around 80 bacterial and fungal PET-active enzymes (PETases) are known, originating from four bacterial and two fungal phyla. In contrast, no archaeal enzyme had been identified to degrade PET. Here we report on the structural and biochemical characterization of PET46 (RLI42440.1), an archaeal promiscuous feruloyl esterase exhibiting degradation activity on semi-crystalline PET powder comparable to IsPETase and LCC (wildtypes), and higher activity on bis-, and mono-(2-hydroxyethyl) terephthalate (BHET and MHET). The enzyme, found by a sequence-based metagenome search, is derived from a non-cultivated, deep-sea Candidatus Bathyarchaeota archaeon. Biochemical characterization demonstrated that PET46 is a promiscuous, heat-adapted hydrolase. Its crystal structure was solved at a resolution of 1.71 A. It shares the core alpha/beta-hydrolase fold with bacterial PETases, but contains a unique lid common in feruloyl esterases, which is involved in substrate binding. Thus, our study widens the currently known diversity of PET-hydrolyzing enzymes, by demonstrating PET depolymerization by a plant cell wall-degrading esterase.
ESTHER : Perez-Garcia_2023_Commun.Chem_6_193
PubMedSearch : Perez-Garcia_2023_Commun.Chem_6_193
PubMedID: 37697032
Gene_locus related to this paper: 9arch-PETcan211 , 9cren-PETcan204 , 9arch-PET46

Title : Andean soil-derived lignocellulolytic bacterial consortium as a source of novel taxa and putative plastic-active enzymes - Diaz-Garcia_2023_Syst.Appl.Microbiol_47_126485
Author(s) : Diaz-Garcia L , Chuvochina M , Feuerriegel G , Bunk B , Sproer C , Streit WR , Rodriguez RL , Overmann J , Jimenez DJ
Ref : Syst Appl Microbiol , 47 :126485 , 2023
Abstract : An easy and straightforward way to engineer microbial environmental communities is by setting up liquid enrichment cultures containing a specific substrate as the sole source of carbon. Here, we analyzed twenty single-contig high-quality metagenome-assembled genomes (MAGs) retrieved from a microbial consortium (T6) that was selected by the dilution-to-stimulation approach using Andean soil as inoculum and lignocellulose as a selection pressure. Based on genomic metrics (e.g., average nucleotide and amino acid identities) and phylogenomic analyses, 15 out of 20 MAGs were found to represent novel bacterial species, with one of those (MAG_26) belonging to a novel genus closely related to Caenibius spp. (Sphingomonadaceae). Following the rules and requirements of the SeqCode, we propose the name Andeanibacterium colombiense gen. nov., sp. nov. for this taxon. A subsequent functional annotation of all MAGs revealed that MAG_7 (Pseudobacter hemicellulosilyticus sp. nov.) contains 20, 19 and 16 predicted genes from carbohydrate-active enzymes families GH43, GH2 and GH92, respectively. Its lignocellulolytic gene profile resembles that of MAG_2 (the most abundant member) and MAG_3858, both of which belong to the Sphingobacteriaceae family. Using a database that contains experimentally verified plastic-active enzymes (PAZymes), twenty-seven putative bacterial polyethylene terephthalate (PET)-active enzymes (i.e., alpha/beta-fold hydrolases) were detected in all MAGs. A maximum of five putative PETases were found in MAG_3858, and two PETases were found to be encoded by A. colombiense. In conclusion, we demonstrate that lignocellulose-enriched liquid cultures coupled with genome-resolved metagenomics are suitable approaches to unveil the hidden bacterial diversity and its polymer-degrading potential in Andean soil ecosystems.
ESTHER : Diaz-Garcia_2023_Syst.Appl.Microbiol_47_126485
PubMedSearch : Diaz-Garcia_2023_Syst.Appl.Microbiol_47_126485
PubMedID: 38211536

Title : The metagenome-derived esterase PET40 is highly promiscuous and hydrolyses polyethylene terephthalate (PET) - Zhang_2023_Febs.j__
Author(s) : Zhang H , Dierkes RF , Perez-Garcia P , Costanzi E , Dittrich J , Cea PA , Gurschke M , Applegate V , Partus K , Schmeisser C , Pfleger C , Gohlke H , Smits SHJ , Chow J , Streit WR
Ref : Febs J , : , 2023
Abstract : Polyethylene terephthalate (PET) is a widely used synthetic polymer and known to contaminate marine and terrestrial ecosystems. Only few PET-active microorganisms and enzymes (PETases) are currently known and it is debated whether degradation activity for PET originates from promiscuous enzymes with broad substrate spectra that primarily act on natural polymers or other bulky substrates, or whether microorganisms evolved their genetic makeup to accepting PET as a carbon source. Here, we present a predicted diene lactone hydrolase designated PET40, which acts on a broad spectrum of substrates, including PET. It is the first esterase with activity on PET from a GC-rich Gram-positive Amycolatopsis species belonging to the Pseudonocardiaceae (Actinobacteria). It is highly conserved within the genera Amycolatopsis and Streptomyces. PET40 was identified by sequence-based metagenome search using a PETase-specific Hidden Markov Model (HMM). Besides acting on PET, PET40 has a versatile substrate spectrum, hydrolyzing delta-lactones, beta-lactam antibiotics, the polyester-polyurethane Impranil(a) DLN, and various para-nitrophenyl (pNP) ester substrates. Molecular docking suggests that the PET degradative activity is likely a result of the promiscuity of PET40, as potential binding modes were found for substrates encompassing mono(2-hydroxyethyl) terephthalate (MHET), bis(2-hydroxyethyl) terephthalate (BHET), and a PET trimer (PET(3) ). We also solved the crystal structure of the inactive PET40 variant S178A to 1.60 A resolution. PET40 is active throughout a wide pH (pH 4-10) and temperature range (4-65 degreesC) and remarkably stable in the presence of 5% sodium dodecyl sulfate (SDS), making it a promising enzyme as a starting point for further investigations and optimization approaches.
ESTHER : Zhang_2023_Febs.j__
PubMedSearch : Zhang_2023_Febs.j__
PubMedID: 37549040
Gene_locus related to this paper: 9pseu-PET40

Title : Metagenomic Screening of a Novel PET Esterase via In Vitro Expression System - Han_2023_Methods.Mol.Biol_2555_167
Author(s) : Han Y , Dierkes RF , Streit WR
Ref : Methods Mol Biol , 2555 :167 , 2023
Abstract : Metagenomic screening is a widely applied biotechnological approach for screening of novel industrial enzymes. The traditional method of metagenomic screening is based on the functional analyses of heterologously expressed environmental genes in a suitable host, which is the bottleneck of this method. To avoid limitation from the clone-dependent system, an in vitro expression technology has been developed in combination with next-generation sequencing and bioinformatics. First, the sequence profile of a target enzyme, e.g., poly(ethylene terephthalate) esterase in this protocol, is constructed according to the sequences of well-characterized enzymes. Then, the sequence screening is performed with this computationally generated profile among all available metagenomic databases. Afterwards, the candidate genes are synthesized and expressed in vitro with RNA polymerase and translation machinery from special cell extract. Finally, such in vitro produced enzymes are directly applied for the functional analyses. Comparing to the traditional screening methods, this in vitro screening technology can not only save time and materials, but also be easily developed for high-throughput screening with an automatic pipetting robot.
ESTHER : Han_2023_Methods.Mol.Biol_2555_167
PubMedSearch : Han_2023_Methods.Mol.Biol_2555_167
PubMedID: 36306086

Title : The PET-Degrading Potential of Global Metagenomes: From In Silico Mining to Active Enzymes - Chow_2023_Methods.Mol.Biol_2555_139
Author(s) : Chow J , Perez-Garcia P , Dierkes RF , Zhang H , Streit WR
Ref : Methods Mol Biol , 2555 :139 , 2023
Abstract : Against the background of the steadily increasing amount of plastic waste in the sea and on land, it is more important than ever to find ways out of this situation. In recent years, microorganisms have been discovered that are capable of degrading artificial polymers such as polyethylene terephthalate (PET). Even if the turnover rates of the enzymes responsible for this reaction may be too low to solve the global plastic pollution problem, it is still of great societal interest to find microorganisms that are able to degrade the polymer. The corresponding enzymes, PET esterases (PETases) can be used in biotechnological processes and could contribute to a resource-saving circular economy. In this chapter, we present a sequence-based in silico screening method to find new PETases in metagenomic datasets. This method can easily be adapted to find other enzyme classes. We also list a number of assays that can be used to test the enzymes for activity on PET as well as other substrates.
ESTHER : Chow_2023_Methods.Mol.Biol_2555_139
PubMedSearch : Chow_2023_Methods.Mol.Biol_2555_139
PubMedID: 36306084

Title : A phospholipase B from Pseudomonas aeruginosa with activity towards endogenous phospholipids affects biofilm assembly - Weiler_2022_Biochim.Biophys.Acta.Mol.Cell.Biol.Lipids_1867_159101
Author(s) : Weiler AJ , Spitz O , Gudzuhn M , Schott-Verdugo SN , Kamel M , Thiele B , Streit WR , Kedrov A , Schmitt L , Gohlk H , Kovacic F , Gohlke H
Ref : Biochimica & Biophysica Acta Molecular & Cellular Biology Lipids , 1867 :159101 , 2022
Abstract : Pseudomonas aeruginosa is a severe threat to immunocompromised patients due to its numerous virulence factors and biofilm-mediated multidrug resistance. It produces and secretes various toxins with hydrolytic activities including phospholipases. However, the function of intracellular phospholipases for bacterial virulence has still not been established. Here, we demonstrate that the hypothetical gene pa2927 of P. aeruginosa encodes a novel phospholipase B named PaPlaB. At reaction equilibrium, PaPlaB purified from detergent-solubilized membranes of E. coli released fatty acids (FAs) from sn-1 and sn-2 positions of phospholipids at the molar ratio of 51:49. PaPlaB in vitro hydrolyzed P. aeruginosa phospholipids reconstituted in detergent micelles and phospholipids reconstituted in vesicles. Cellular localization studies indicate that PaPlaB is a cell-bound PLA of P. aeruginosa and that it is peripherally bound to both membranes in E. coli, yet the active form was predominantly associated with the cytoplasmic membrane of E. coli. Decreasing the concentration of purified and detergent-stabilized PaPlaB leads to increased enzymatic activity, and at the same time triggers oligomer dissociation. We showed that the free FA profile, biofilm amount and architecture of the wild type and deltaplaB differ. However, it remains to be established how the PLB activity of PaPlaB is regulated by homooligomerisation and how it relates to the phenotype of the P. aeruginosa deltaplaB. This novel putative virulence factor contributes to our understanding of phospholipid degrading enzymes and might provide a target for new therapeutics against P. aeruginosa biofilms.
ESTHER : Weiler_2022_Biochim.Biophys.Acta.Mol.Cell.Biol.Lipids_1867_159101
PubMedSearch : Weiler_2022_Biochim.Biophys.Acta.Mol.Cell.Biol.Lipids_1867_159101
PubMedID: 35063652
Gene_locus related to this paper: pseae-PA2927

Title : An Ultra-Sensitive Comamonas thiooxidans Biosensor for the Rapid Detection of Enzymatic Polyethylene Terephthalate (PET) Degradation - Dierkes_2022_Appl.Environ.Microbiol__e0160322
Author(s) : Dierkes RF , Wypych A , Perez-Garcia P , Danso D , Chow J , Streit WR
Ref : Applied Environmental Microbiology , :e0160322 , 2022
Abstract : Polyethylene terephthalate (PET) is a prevalent synthetic polymer that is known to contaminate marine and terrestrial environments. Currently, only a limited number of PET-active microorganisms and enzymes (PETases) are known. This is in part linked to the lack of highly sensitive function-based screening assays for PET-active enzymes. Here, we report on the construction of a fluorescent biosensor based on Comamonas thiooxidans strain S23. C. thiooxidans S23 transports and metabolizes TPA, one of the main breakdown products of PET, using a specific tripartite tricarboxylate transporter (TTT) and various mono- and dioxygenases encoded in its genome in a conserved operon ranging from tphC-tphA1. TphR, an IclR-type transcriptional regulator is found upstream of the tphC-tphA1 cluster where TPA induces transcription of tphC-tphA1 up to 88-fold in exponentially growing cells. In the present study, we show that the C. thiooxidans S23 wild-type strain, carrying the sfGFP gene fused to the tphC promoter, senses TPA at concentrations as low as 10 microM. Moreover, a deletion mutant lacking the catabolic genes involved in TPA degradation thphA2-A1 (deltatphA2A3BA1) is up to 10,000-fold more sensitive and detects TPA concentrations in the nanomolar range. This is, to our knowledge, the most sensitive reporter strain for TPA and we demonstrate that it can be used for the detection of enzymatic PET breakdown products. IMPORTANCE Plastics and microplastics accumulate in all ecological niches. The construction of more sensitive biosensors allows to monitor and screen potential PET degradation in natural environments and industrial samples. These strains will also be a valuable tool for functional screenings of novel PETase candidates and variants or monitoring of PET recycling processes using biocatalysts. Thereby they help us to enrich the known biodiversity and efficiency of PET degrading organisms and enzymes and understand their contribution to environmental plastic degradation.
ESTHER : Dierkes_2022_Appl.Environ.Microbiol__e0160322
PubMedSearch : Dierkes_2022_Appl.Environ.Microbiol__e0160322
PubMedID: 36507653

Title : Plastics degradation by hydrolytic enzymes: The plastics-active enzymes database-PAZy - Buchholz_2022_Proteins_90_1443
Author(s) : Buchholz PCF , Feuerriegel G , Zhang H , Perez-Garcia P , Nover LL , Chow J , Streit WR , Pleiss J
Ref : Proteins , 90 :1443 , 2022
Abstract : Petroleum-based plastics are durable and accumulate in all ecological niches. Knowledge on enzymatic degradation is sparse. Today, less than 50 verified plastics-active enzymes are known. First examples of enzymes acting on the polymers polyethylene terephthalate (PET) and polyurethane (PUR) have been reported together with a detailed biochemical and structural description. Furthermore, very few polyamide (PA) oligomer active enzymes are known. In this article, the current known enzymes acting on the synthetic polymers PET and PUR are briefly summarized, their published activity data were collected and integrated into a comprehensive open access database. The Plastics-Active Enzymes Database (PAZy) represents an inventory of known and experimentally verified enzymes that act on synthetic fossil fuel-based polymers. Almost 3000 homologs of PET-active enzymes were identified by profile hidden Markov models. Over 2000 homologs of PUR-active enzymes were identified by BLAST. Based on multiple sequence alignments, conservation analysis identified the most conserved amino acids, and sequence motifs for PET- and PUR-active enzymes were derived.
ESTHER : Buchholz_2022_Proteins_90_1443
PubMedSearch : Buchholz_2022_Proteins_90_1443
PubMedID: 35175626

Title : Investigation of the halophilic PET hydrolase PET6 from Vibrio gazogenes - Weigert_2022_Protein.Sci__e4500
Author(s) : Weigert S , Perez-Garcia P , Gisdon FJ , Gagsteiger A , Schweinshaut K , Ullmann GM , Chow J , Streit WR , Hcker B
Ref : Protein Science , :e4500 , 2022
Abstract : The handling of plastic waste and the associated ubiquitous occurrence of microplastic poses one of the biggest challenges of our time. Recent investigations of plastic degrading enzymes have opened new prospects for biological microplastic decomposition as well as recycling applications. For polyethylene terephthalate, in particular, several natural and engineered enzymes are known to have such promising properties. From a previous study that identified new PETase candidates by homology search, we chose the candidate PET6 from the globally distributed, halophilic organism Vibrio gazogenes for further investigation. By mapping the occurrence of Vibrios containing PET6 homologs we demonstrated their ubiquitous prevalence in the pangenome of several Vibrio strains. The biochemical characterization of PET6 showed that PET6 has a comparatively lower activity than other enzymes but also revealed a superior turnover at very high salt concentrations. The crystal structure of PET6 provides structural insights into this adaptation to saline environments. By grafting only a few beneficial mutations from other PET degrading enzymes onto PET6, we increased the activity up to three-fold, demonstrating the evolutionary potential of the enzyme. MD simulations of the variant helped rationalize the mutational effects of those mutants and elucidate the interaction of the enzyme with a PET substrate. With tremendous amounts of plastic waste in the Ocean and the prevalence of Vibrio gazogenes in marine biofilms and estuarine marshes, our findings suggest that Vibrio and the PET6 enzyme are worthy subjects to study the PET degradation in marine environments. This article is protected by copyright. All rights reserved.
ESTHER : Weigert_2022_Protein.Sci__e4500
PubMedSearch : Weigert_2022_Protein.Sci__e4500
PubMedID: 36336469
Gene_locus related to this paper: vibga-a0a1m5fok3

Title : Exploring the global metagenome for plastic-degrading enzymes - Perez-Garcia_2021_Methods.Enzymol_648_137
Author(s) : Perez-Garcia P , Danso D , Zhang H , Chow J , Streit WR
Ref : Methods Enzymol , 648 :137 , 2021
Abstract : Plastics are extensively used in our daily life, but they are also a major pollutant of our biosphere accumulating in both the ocean and the land. In the recent years, few enzymes and microorganisms have been discovered with the ability to degrade even fewer synthetic polymers. Nevertheless, more active species and enzymes need to be discovered and described in order to gain more knowledge about protein adaptation to the degradation of not-naturally-occurring polymers. Within this chapter, we focus on efficient methods to identify novel polyethylene terephthalate-degrading enzymes (PETases) from culturable and non-culturable microorganisms by a combination of sequence- and function-based screening. This protocol can be adapted to discover other plastic hydrolases and in general for other enzymes, for which not many characterized specimens are yet available.
ESTHER : Perez-Garcia_2021_Methods.Enzymol_648_137
PubMedSearch : Perez-Garcia_2021_Methods.Enzymol_648_137
PubMedID: 33579401

Title : Plastics degradation by hydrolytic enzymes: the Plastics-Active Enzymes Database - PAZy - Buchholz_2021_Authorea__
Author(s) : Buchholz PCF , Zhang H , Perez-Garcia P , Nover LL , Chow J , Streit WR , Pleiss J
Ref : Authorea , : , 2021
Abstract : Petroleum based plastics are durable and accumulate in all ecological niches. Knowledge on enzymatic degradation is sparse. Today, less than 50 verified plastics-active enzymes are known. First examples of enzymes acting on the polymers polyethylene terephthalate (PET) and polyurethane (PUR) have been reported together with a detailed biochemical and structural description. Further, very few polyamide (PA) oligomer active enzymes are known. In this paper, the current known enzymes acting on the synthetic polymers PET and PUR are briefly summarized, their published activity data were collected and integrated into a comprehensive open access database. The Plastics-Active Enzymes Database (PAZy) represents an inventory of known and experimentally verified plastics-active enzymes. Almost 3000 homologues of PET-active enzymes were identified by profile hidden Markov models. Over 2000 homologues of PUR-active enzymes were identified by BLAST. Based on multiple sequence alignments, conservation analysis identified the most conserved amino acids, and sequence motifs for PET- and PUR-active enzymes were derived.
ESTHER : Buchholz_2021_Authorea__
PubMedSearch : Buchholz_2021_Authorea__
PubMedID:

Title : The abundance of mRNA transcripts of bacteroidetal polyethylene terephthalate (PET) esterase genes may indicate a role in marine plastic degradation - Zhang_2021_ResearchSquare__
Author(s) : Zhang H , Dierkes R , Perez-Garcia P , Weigert S , Sternagel S , Hallam S , Schott T , Juergens K , Vollstedt C , Chibani C , Danso D , Buchholz PCF , Pleiss J , Almeida A , Hocker B , Schmitz R , Chow J , Streit WR
Ref : ResearchSquare , : , 2021
Abstract : https://www.researchsquare.com/article/rs-567691/v2 Polyethylene terephthalate (PET) is an important synthetic polymer accumulating in nature 2 and recent studies have identified microorganisms capable of degrading PET. While the majority of 3 known PET hydrolases originate from the Actinobacteria and Proteobacteria, here we describe the 4 first functional PET-active enzymes from the Bacteroidetes phylum. Using a PETase-specific 5 Hidden-Markov-Model (HMM)-based search algorithm we identified two promiscuous and cold6 active esterases derived from Aequorivita sp. (PET27) and Chryseobacterium jeonii (PET30) acting 7 on PET foil and powder. Notably, one of the enzymes (PET30) was able to hydrolyze PET at 8 temperatures between 4 - 30 C with a similar turnover rate compared to the well-known Ideonella 9 sakaiensis enzyme (IsPETase). 10 PET27 and PET30 homologues were detected in metagenomes encompassing a wide range 11 of different global climate zones. Additional transcript abundance mapping of marine samples imply 12 that these promiscuous enzymes and source organisms may play a role in the long-term 13 degradation of microplastic particles and fibers.
ESTHER : Zhang_2021_ResearchSquare__
PubMedSearch : Zhang_2021_ResearchSquare__
PubMedID:
Gene_locus related to this paper: flutr-f2ie04 , 9flao-a0a0c1f4u8 , 9flao-kjj39608 , 9flao-a0a1m6f5v0 , 9flao-a0a330mq60

Title : The Bacteroidetes Aequorivita sp. and Kaistella jeonii Produce Promiscuous Esterases With PET-Hydrolyzing Activity - Zhang_2022_Front.Microbiol_12_803896
Author(s) : Zhang H , Perez-Garcia P , Dierkes RF , Applegate V , Schumacher J , Chibani CM , Sternagel S , Preuss L , Weigert S , Schmeisser C , Danso D , Pleiss J , Almeida A , Hocker B , Hallam SJ , Schmitz RA , Smits SHJ , Chow J , Streit WR
Ref : Front Microbiol , 12 :803896 , 2021
Abstract : Certain members of the Actinobacteria and Proteobacteria are known to degrade polyethylene terephthalate (PET). Here, we describe the first functional PET-active enzymes from the Bacteroidetes phylum. Using a PETase-specific Hidden-Markov-Model- (HMM-) based search algorithm, we identified several PETase candidates from Flavobacteriaceae and Porphyromonadaceae. Among them, two promiscuous and cold-active esterases derived from Aequorivita sp. (PET27) and Kaistella jeonii (PET30) showed depolymerizing activity on polycaprolactone (PCL), amorphous PET foil and on the polyester polyurethane Impranil((a)) DLN. PET27 is a 37.8 kDa enzyme that released an average of 174.4 nmol terephthalic acid (TPA) after 120 h at 30 degreesC from a 7 mg PET foil platelet in a 200 microl reaction volume, 38-times more than PET30 (37.4 kDa) released under the same conditions. The crystal structure of PET30 without its C-terminal Por-domain (PET30deltaPorC) was solved at 2.1 A and displays high structural similarity to the IsPETase. PET30 shows a Phe-Met-Tyr substrate binding motif, which seems to be a unique feature, as IsPETase, LCC and PET2 all contain Tyr-Met-Trp binding residues, while PET27 possesses a Phe-Met-Trp motif that is identical to Cut190. Microscopic analyses showed that K. jeonii cells are indeed able to bind on and colonize PET surfaces after a few days of incubation. Homologs of PET27 and PET30 were detected in metagenomes, predominantly aquatic habitats, encompassing a wide range of different global climate zones and suggesting a hitherto unknown influence of this bacterial phylum on man-made polymer degradation.
ESTHER : Zhang_2022_Front.Microbiol_12_803896
PubMedSearch : Zhang_2022_Front.Microbiol_12_803896
PubMedID: 35069509
Gene_locus related to this paper: flutr-f2ie04 , 9flao-a0a0c1f4u8 , 9flao-kjj39608 , 9flao-a0a330mq60

Title : Plastics: Environmental and Biotechnological Perspectives on Microbial Degradation - Danso_2019_Appl.Environ.Microbiol_85_e01095
Author(s) : Danso D , Chow J , Streit WR
Ref : Applied Environmental Microbiology , 85 : , 2019
Abstract : Plastics are widely used in the global economy, and each year, at least 350 to 400 million tons are being produced. Due to poor recycling and low circular use, millions of tons accumulate annually in terrestrial or marine environments. Today it has become clear that plastic causes adverse effects in all ecosystems and that microplastics are of particular concern to our health. Therefore, recent microbial research has addressed the question of if and to what extent microorganisms can degrade plastics in the environment. This review summarizes current knowledge on microbial plastic degradation. Enzymes available act mainly on the high-molecular-weight polymers of polyethylene terephthalate (PET) and ester-based polyurethane (PUR). Unfortunately, the best PUR- and PET-active enzymes and microorganisms known still have moderate turnover rates. While many reports describing microbial communities degrading chemical additives have been published, no enzymes acting on the high-molecular-weight polymers polystyrene, polyamide, polyvinylchloride, polypropylene, ether-based polyurethane, and polyethylene are known. Together, these polymers comprise more than 80% of annual plastic production. Thus, further research is needed to significantly increase the diversity of enzymes and microorganisms acting on these polymers. This can be achieved by tapping into the global metagenomes of noncultivated microorganisms and dark matter proteins. Only then can novel biocatalysts and organisms be delivered that allow rapid degradation, recycling, or value-added use of the vast majority of most human-made polymers.
ESTHER : Danso_2019_Appl.Environ.Microbiol_85_e01095
PubMedSearch : Danso_2019_Appl.Environ.Microbiol_85_e01095
PubMedID: 31324632

Title : The Thaumarchaeon N. gargensis carries functional bioABD genes and has a promiscuous E. coli DeltabioH-complementing esterase EstN1 - Chow_2018_Sci.Rep_8_13823
Author(s) : Chow J , Danso D , Ferrer M , Streit WR
Ref : Sci Rep , 8 :13823 , 2018
Abstract : Biotin is an essential cofactor required for carboxylation and decarboxylation reactions in all domains of life. While biotin biosynthesis in most Bacteria and Eukarya is well studied, the complete pathway for this vitamer in Archaea is still not known. Detailed genome searches indicated the presence of possible bio gene clusters only in Methanococcales and Thaumarchaeota. Therefore, we analysed the functionality of the predicted genes bioA, bioB, bioD and bioF in the Thaumarchaeon Nitrososphaera gargensis Ga2.9 which are essential for the later steps of biotin synthesis. In complementation tests, the gene cluster-encoded N. gargensis bioABD genes except bioF restored growth of corresponding E. coli Rosetta-gami 2 (DE3) deletion mutants. To find out how biotin biosynthesis is initiated, we searched the genome for a possible bioH analogue encoding a pimeloyl-ACP-methylester carboxylesterase. The respective amino acid sequence of the ORF estN1 showed weak conserved domain similarity to this class of enzymes (e-value 3.70e(-42)). Remarkably, EstN1 is a promiscuous carboxylesterase that complements E. coli DeltabioH and Mesorhizobium loti DeltabioZ mutants for growth on biotin-free minimal medium. Additional 3D-structural models support the hypothesis that EstN1 is a BioH analogue. Thus, this is the first report providing experimental evidence that Archaea carry functional bio genes.
ESTHER : Chow_2018_Sci.Rep_8_13823
PubMedSearch : Chow_2018_Sci.Rep_8_13823
PubMedID: 30218044

Title : Determinants and prediction of esterase substrate promiscuity patterns - Martinez-Martinez_2018_ACS.Chem.Biol_13_225
Author(s) : Martinez-Martinez M , Coscolin C , Santiago G , Chow J , Stogios PJ , Bargiela R , Gertler C , Navarro-Fernandez J , Bollinger A , Thies S , Mendez-Garcia C , Popovic A , Brown G , Chernikova TN , Garcia-Moyano A , Bjergah GE , Perez-Garcia P , Hai T , Del Pozo MV , Stokke R , Steen IH , Cui H , Xu X , Nocek BP , Alcaide M , Distaso M , Mesa V , Pelaez AI , Sanchez J , Buchholz PCF , Pleiss J , Fernandez-Guerra A , Glockner FO , Golyshina OV , Yakimov MM , Savchenko A , Jaeger KE , Yakunin AF , Streit WR , Golyshin PN , Guallar V , Ferrer M
Ref : ACS Chemical Biology , 13 :225 , 2018
Abstract : Esterases receive special attention because their wide distribution in biological systems and environments and their importance for physiology and chemical synthesis. The prediction of esterases substrate promiscuity level from sequence data and the molecular reasons why certain such enzymes are more promiscuous than others, remain to be elucidated. This limits the surveillance of the sequence space for esterases potentially leading to new versatile biocatalysts and new insights into their role in cellular function. Here we performed an extensive analysis of the substrate spectra of 145 phylogenetically and environmentally diverse microbial esterases, when tested with 96 diverse esters. We determined the primary factors shaping their substrate range by analyzing substrate range patterns in combination with structural analysis and protein-ligand simulations. We found a structural parameter that helps ranking (classifying) promiscuity level of esterases from sequence data at 94% accuracy. This parameter, the active site effective volume, exemplifies the topology of the catalytic environment by measuring the active site cavity volume corrected by the relative solvent accessible surface area (SASA) of the catalytic triad. Sequences encoding esterases with active site effective volumes (cavity volume/SASA) above a threshold show greater substrate spectra, which can be further extended in combination with phylogenetic data. This measure provides also a valuable tool for interrogating substrates capable of being converted. This measure, found to be transferred to phosphatases of the haloalkanoic acid dehalogenase superfamily and possibly other enzymatic systems, represents a powerful tool for low-cost bioprospecting for esterases with broad substrate ranges, in large scale sequence datasets.
ESTHER : Martinez-Martinez_2018_ACS.Chem.Biol_13_225
PubMedSearch : Martinez-Martinez_2018_ACS.Chem.Biol_13_225
PubMedID: 29182315
Gene_locus related to this paper: 9zzzz-a0a2k8jn75 , 9zzzz-a0a2k8jt94 , 9zzzz-a0a0g3fj44 , 9zzzz-a0a0g3fh10 , 9zzzz-a0a0g3fh03 , 9bact-a0a1s5qkj8 , 9zzzz-a0a0g3feh5 , 9zzzz-a0a0g3fkz4 , 9zzzz-a0a0g3fh07 , 9zzzz-a0a0g3fh34 , 9zzzz-a0a0g3fh31 , 9bact-KY458167 , alcbs-q0vqa3 , 9bact-a0a1s5qki8 , 9zzzz-a0a0g3feq8 , 9zzzz-a0a0g3feh8 , 9zzzz-a0a0g3fh19 , 9bact-KY203037 , 9bact-a0a1s5ql22 , 9bact-a0a1s5qm34 , 9bact-KY203034 , 9bact-r9qzg0 , 9bact-a0a1s5qly8 , 9zzzz-a0a0g3fkz8 , 9zzzz-a0a0g3feg9 , 9zzzz-KY203033 , 9zzzz-a0a0g3fes4 , 9zzzz-a0a0g3fh42 , 9bact-a0a1s5qlx2 , 9zzzz-KY483651 , 9bact-a0a1s5qmh4 , 9zzzz-KY203032 , 9zzzz-EH87 , 9zzzz-a0a0g3fei1 , 9zzzz-a0a0g3fet2 , 9zzzz-KY483647 , 9zzzz-EH82 , 9zzzz-a0a0g3fe15 , 9bact-KY203031 , 9bact-t1w006 , 9zzzz-a0a0g3fet6 , 9bact-KY458164 , geoth-g8myf3 , 9bact-a0a1s5ql04 , 9gamm-a0a1y0ihk7 , 9bact-a0a1s5qly6 , 9bact-a0a1s5qkg4 , 9bact-a0a1s5qkm4 , 9gamm-s5tv80 , 9gamm-a0a0c4zhg2 , 9zzzz-t1b379 , 9gamm-KY483646 , 9bact-KY458160 , 9zzzz-a0a0g3fj57 , 9gamm-s5t8349 , 9arch-KY203036 , 9bact-KY458168 , 9zzzz-a0a0g3fes0 , 9zzzz-t1be47 , 9bact-KY458159 , 9zzzz-a0a0g3fh39 , 9bact-t1vzd5 , 9prot-EH41 , 9bact-Lip114 , alcbs-q0vt77 , 9bact-a0a1s5qke6 , 9bact-a0a1s5qkf3 , 9prot-SRP030024 , 9gamm-s5t532 , 9bact-a0a1s5qkl2 , 9bact-a0a1s5qkk8 , 9zzzz-KY203030 , 9zzzz-t1d4I7 , 9prot-KY019260 , 9bact-a0a1s5qm38 , 9arch-KY458161 , 9prot-KY010302 , 9zzzz-a0a0g3fl25 , 9actn-KY010298 , 9gamm-s5u059 , 9bact-a0a1s5qmi7 , 9bact-KY010297 , 9bact-KY483642 , 9bact-a0a1s5qkj1 , 9bact-KY010299 , 9bact-KY483648 , alcbs-q0vtl7 , 9bact-a0a1s5qf1 , 9bact-a0a1s5qkg0 , 9bact-a0a0h4tgu6 , 9bact-MilE3 , 9bact-LAE6 , 9alte-MGS-MT1 , 9bact-r9qzf7 , 9gamm-k0c6t6 , alcbs-q0vl36 , alcbs-q0vlq1 , alcbs-q0vq49 , bacsu-pnbae , canar-LipB , canan-lipasA , geost-lipas , marav-a1u5n0 , pseps-i7k8x5 , staep-GEHD , symth-q67mr3 , altma-s5cfn7 , cycsp-k0c2b8 , alcbs-q0vlk5 , 9bact-k7qe48 , 9bact-MGS-M1 , 9bact-MGS-M2 , 9bact-a0a0b5kns5 , 9zzzz-a0a0g3fej4 , 9zzzz-a0a0g3fj60 , 9zzzz-a0a0g3fej0 , 9zzzz-a0a0g3fj64 , 9bact-a0a0b5kc16 , 9zzzz-a0a0g3feg6 , 9zzzz-a0a0g3feu6

Title : New insights into the function and global distribution of polyethylene terephthalate (PET) degrading bacteria and enzymes in marine and terrestrial metagenomes - Danso_2018_Appl.Environ.Microbiol_84_e2773
Author(s) : Danso D , Schmeisser C , Chow J , Zimmermann W , Wei R , Leggewie C , Li X , Hazen T , Streit WR
Ref : Applied Environmental Microbiology , 84 :e2773 , 2018
Abstract : Polyethylene terephthalate (PET) is one of the most important synthetic polymers used nowadays. Unfortunately, the polymers accumulate in nature and until now, no highly active enzymes are known that can degrade it at high velocity. Enzymes involved in PET degradation are mainly alpha/beta-hydrolases like cutinases and related enzymes (E.C. 3.1.-). Currently, only a small number of such enzymes are well characterized. Within this work, a search algorithm was developed that identified 504 possible PET hydrolase candidate genes from various databases. A further global search that comprised more than 16 GB of sequence information within 108 marine and 25 terrestrial metagenomes obtained from the IMG data base detected 349 putative PET hydrolases. Heterologous expression of four such candidate enzymes verified the function of these enzymes and confirmed the usefulness of the developed search algorithm. Thereby, two novel and thermostable enzymes with high potential for downstream application were in part characterized. Clustering of 504 novel enzyme candidates based on amino acid similarities indicated that PET hydrolases mainly occur in the phylum of Actinobacteria, Proteobacteria and Bacteroidetes Within the Proteobacteria, the Beta-, Delta- and Gammaproteobacteria were the main hosts. Remarkably enough, in the marine environment, bacteria affiliated with the phylum of the Bacteroidetes appear to be the main host of PET hydrolase genes rather than Actinobacteria or Proteobacteria as observed for the terrestrial metagenomes. Our data further imply that PET hydrolases are truly rare enzymes. The highest occurrence of 1.5 hits/Mb was observed in a sample site containing crude oil.IMPORTANCE Polyethylene terephthalate (PET) accumulates in our environment without significant microbial conversion. Although few PET hydrolases are already known it is still unknown how frequent they appear and which main bacterial phyla they are affiliated with. In this study, deep sequence mining of protein databases and metagenomes demonstrated that PET hydrolases indeed are occurring at very low frequencies in the environment. Further it was possible to link them to phyla which were previously unknown to harbor such enzymes. This work contributes novel knowledge to the phylogenetic relationship, the recent evolution and the global distribution of PET hydrolases. Finally, we describe biochemical traits of four novel PET hydrolases.
ESTHER : Danso_2018_Appl.Environ.Microbiol_84_e2773
PubMedSearch : Danso_2018_Appl.Environ.Microbiol_84_e2773
PubMedID: 29427431
Gene_locus related to this paper: 9burk-PET10 , 9burk-PET11 , 9gamm-a0a0d4l7e6 , 9alte-n6vy44 , 9zzzz-a0a0f9x315 , deiml-e8u721 , olean-r4ykl9 , vibga-a0a1z2siq1 , 9burk-a0a0g3bi90 , 9bact-c3ryl0 , 9actn-h6wx58 , idesa-peth , 9bact-g9by57 , acide-PBSA , morsp-lip1

Title : Molecular Keys to the Janthinobacterium and Duganella spp. Interaction with the Plant Pathogen Fusarium graminearum - Haack_2016_Front.Microbiol_7_1668
Author(s) : Haack FS , Poehlein A , Kroger C , Voigt CA , Piepenbring M , Bode HB , Daniel R , Schafer W , Streit WR
Ref : Front Microbiol , 7 :1668 , 2016
Abstract : Janthinobacterium and Duganella are well-known for their antifungal effects. Surprisingly, almost nothing is known on molecular aspects involved in the close bacterium-fungus interaction. To better understand this interaction, we established the genomes of 11 Janthinobacterium and Duganella isolates in combination with phylogenetic and functional analyses of all publicly available genomes. Thereby, we identified a core and pan genome of 1058 and 23,628 genes. All strains encoded secondary metabolite gene clusters and chitinases, both possibly involved in fungal growth suppression. All but one strain carried a single gene cluster involved in the biosynthesis of alpha-hydroxyketone-like autoinducer molecules, designated JAI-1. Genome-wide RNA-seq studies employing the background of two isolates and the corresponding JAI-1 deficient strains identified a set of 45 QS-regulated genes in both isolates. Most regulated genes are characterized by a conserved sequence motif within the promoter region. Among the most strongly regulated genes were secondary metabolite and type VI secretion system gene clusters. Most intriguing, co-incubation studies of J. sp. HH102 or its corresponding JAI-1 synthase deletion mutant with the plant pathogen Fusarium graminearum provided first evidence of a QS-dependent interaction with this pathogen.
ESTHER : Haack_2016_Front.Microbiol_7_1668
PubMedSearch : Haack_2016_Front.Microbiol_7_1668
PubMedID: 27833590
Gene_locus related to this paper: 9burk-a0a1e7w6l2 , 9burk-a0a1e7wlu5

Title : A novel thermoalkalostable esterase from Acidicaldus sp. strain USBA-GBX-499 with enantioselectivity isolated from an acidic hot springs of Colombian Andes - Lopez_2014_Appl.Microbiol.Biotechnol_98_8603
Author(s) : Lopez G , Chow J , Bongen P , Lauinger B , Pietruszka J , Streit WR , Baena S
Ref : Applied Microbiology & Biotechnology , 98 :8603 , 2014
Abstract : Several thermo- and mesoacidophilic bacterial strains that revealed high lipolytic activity were isolated from water samples derived from acidic hot springs in Los Nevados National Natural Park (Colombia). A novel lipolytic enzyme named 499EST was obtained from the thermoacidophilic alpha-Proteobacterium Acidicaldus USBA-GBX-499. The gene estA encoded a 313-amino-acid protein named 499EST. The deduced amino acid sequence showed the highest identity (58 %) with a putative alpha/beta hydrolase from Acidiphilium sp. (ZP_08632277.1). Sequence alignments and phylogenetic analysis indicated that 499EST is a new member of the bacterial esterase/lipase family IV. The esterase reveals its optimum catalytic activity at 55 degrees C and pH 9.0. Kinetic studies showed that 499EST preferentially hydrolyzed middle-length acyl chains (C6-C8), especially p-nitrophenyl (p-NP) caproate (C6). Its thermostability and activity were strongly enhanced by adding 6 mM FeCl3. High stability in the presence of water-miscible solvents such as dimethyl sulfoxide and glycerol was observed. This enzyme also exhibits stability under harsh environmental conditions and enantioselectivity towards naproxen and ibuprofen esters, yielding the medically relevant (S)-enantiomers. In conclusion, according to our knowledge, 499EST is the first thermoalkalostable esterase derived from a Gram-negative thermoacidophilic bacterium.
ESTHER : Lopez_2014_Appl.Microbiol.Biotechnol_98_8603
PubMedSearch : Lopez_2014_Appl.Microbiol.Biotechnol_98_8603
PubMedID: 24818691
Gene_locus related to this paper: 9prot-a0a068lg40

Title : Cloning, expression, purification and preliminary X-ray analysis of EstN2, a novel archaeal alpha\/beta-hydrolase from Candidatus Nitrososphaera gargensis - Kaljunen_2014_Acta.Crystallogr.F.Struct.Biol.Commun_70_1394
Author(s) : Kaljunen H , Chow J , Streit WR , Mueller-Dieckmann J
Ref : Acta Crystallographica F Struct Biol Commun , 70 :1394 , 2014
Abstract : EstN2 is a novel alpha/beta-hydrolase originating from the ammonia-oxidizing thaumarchaeon Candidatus Nitrososphaera gargensis. The genome of the organism was sequenced and genes conferring putative lipolytic activity were amplified and cloned into Escherichia coli as a heterologous host. Through function-based screening, esterase and lipase activity was detected. A recombinant enzyme designated EstN2 was successfully expressed, purified and crystallized. The crystals belonged to space group I2, with one molecule per asymmetric unit, and diffracted X-rays to 1.5 A resolution.
ESTHER : Kaljunen_2014_Acta.Crystallogr.F.Struct.Biol.Commun_70_1394
PubMedSearch : Kaljunen_2014_Acta.Crystallogr.F.Struct.Biol.Commun_70_1394
PubMedID: 25286947
Gene_locus related to this paper: nitgg-k0im51

Title : Complete Genome Sequence of Geobacillus sp. Strain GHH01, a Thermophilic Lipase-Secreting Bacterium - Wiegand_2013_Genome.Announc_1_e0009213
Author(s) : Wiegand S , Rabausch U , Chow J , Daniel R , Streit WR , Liesegang H
Ref : Genome Announc , 1 :e0009213 , 2013
Abstract : Geobacillus sp. strain GHH01 was isolated during a screening for producers of extracellular thermostable lipases. The completely sequenced and annotated 3.6-Mb genome encodes 3,478 proteins. The strain is genetically equipped to utilize a broad range of different substrates and might develop natural competence.
ESTHER : Wiegand_2013_Genome.Announc_1_e0009213
PubMedSearch : Wiegand_2013_Genome.Announc_1_e0009213
PubMedID: 23618712
Gene_locus related to this paper: geoka-q5l3h0 , geosc-d7d055 , geotn-a4isp0 , geos2-a0a0e0tby6

Title : The Janthinobacterium sp. HH01 genome encodes a homologue of the V. cholerae CqsA and L. pneumophila LqsA autoinducer synthases - Hornung_2013_PLoS.One_8_e55045
Author(s) : Hornung C , Poehlein A , Haack FS , Schmidt M , Dierking K , Pohlen A , Schulenburg H , Blokesch M , Plener L , Jung K , Bonge A , Krohn-Molt I , Utpatel C , Timmermann G , Spieck E , Pommerening-Roser A , Bode E , Bode HB , Daniel R , Schmeisser C , Streit WR
Ref : PLoS ONE , 8 :e55045 , 2013
Abstract : Janthinobacteria commonly form biofilms on eukaryotic hosts and are known to synthesize antibacterial and antifungal compounds. Janthinobacterium sp. HH01 was recently isolated from an aquatic environment and its genome sequence was established. The genome consists of a single chromosome and reveals a size of 7.10 Mb, being the largest janthinobacterial genome so far known. Approximately 80% of the 5,980 coding sequences (CDSs) present in the HH01 genome could be assigned putative functions. The genome encodes a wealth of secretory functions and several large clusters for polyketide biosynthesis. HH01 also encodes a remarkable number of proteins involved in resistance to drugs or heavy metals. Interestingly, the genome of HH01 apparently lacks the N-acylhomoserine lactone (AHL)-dependent signaling system and the AI-2-dependent quorum sensing regulatory circuit. Instead it encodes a homologue of the Legionella- and Vibrio-like autoinducer (lqsA/cqsA) synthase gene which we designated jqsA. The jqsA gene is linked to a cognate sensor kinase (jqsS) which is flanked by the response regulator jqsR. Here we show that a jqsA deletion has strong impact on the violacein biosynthesis in Janthinobacterium sp. HH01 and that a jqsA deletion mutant can be functionally complemented with the V. cholerae cqsA and the L. pneumophila lqsA genes.
ESTHER : Hornung_2013_PLoS.One_8_e55045
PubMedSearch : Hornung_2013_PLoS.One_8_e55045
PubMedID: 23405110
Gene_locus related to this paper: 9burk-l9pl81 , 9burk-l9pql3 , 9burk-l9pc92 , 9burk-l9pf07 , 9burk-l9pgi7 , 9burk-l9p8t0 , 9burk-l9pl28

Title : Complete genome sequence of the broad-host-range strain Sinorhizobium fredii USDA257 - Schuldes_2012_J.Bacteriol_194_4483
Author(s) : Schuldes J , Rodriguez Orbegoso M , Schmeisser C , Krishnan HB , Daniel R , Streit WR
Ref : Journal of Bacteriology , 194 :4483 , 2012
Abstract : Here we announce the complete genome sequence of the symbiotic and nitrogen-fixing bacterium Sinorhizobium fredii USDA257. The genome shares a high degree of sequence similarity with the closely related broad-host-range strains S. fredii NGR234 and HH103. Most strikingly, the USDA257 genome encodes a wealth of secretory systems.
ESTHER : Schuldes_2012_J.Bacteriol_194_4483
PubMedSearch : Schuldes_2012_J.Bacteriol_194_4483
PubMedID: 22843606
Gene_locus related to this paper: rhifr-i3x2k3 , rhifr-i3x2s5 , rhifr-i3xe25

Title : The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations - Spang_2012_Environ.Microbiol_14_3122
Author(s) : Spang A , Poehlein A , Offre P , Zumbragel S , Haider S , Rychlik N , Nowka B , Schmeisser C , Lebedeva EV , Rattei T , Bohm C , Schmid M , Galushko A , Hatzenpichler R , Weinmaier T , Daniel R , Schleper C , Spieck E , Streit WR , Wagner M
Ref : Environ Microbiol , 14 :3122 , 2012
Abstract : The cohort of the ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota is a diverse, widespread and functionally important group of microorganisms in many ecosystems. However, our understanding of their biology is still very rudimentary in part because all available genome sequences of this phylum are from members of the Nitrosopumilus cluster. Here we report on the complete genome sequence of Candidatus Nitrososphaera gargensis obtained from an enrichment culture, representing a different evolutionary lineage of AOA frequently found in high numbers in many terrestrial environments. With its 2.83 Mb the genome is much larger than that of other AOA. The presence of a high number of (active) IS elements/transposases, genomic islands, gene duplications and a complete CRISPR/Cas defence system testifies to its dynamic evolution consistent with low degree of synteny with other thaumarchaeal genomes. As expected, the repertoire of conserved enzymes proposed to be required for archaeal ammonia oxidation is encoded by N. gargensis, but it can also use urea and possibly cyanate as alternative ammonia sources. Furthermore, its carbon metabolism is more flexible at the central pyruvate switch point, encompasses the ability to take up small organic compounds and might even include an oxidative pentose phosphate pathway. Furthermore, we show that thaumarchaeota produce cofactor F420 as well as polyhydroxyalkanoates. Lateral gene transfer from bacteria and euryarchaeota has contributed to the metabolic versatility of N. gargensis. This organisms is well adapted to its niche in a heavy metal-containing thermal spring by encoding a multitude of heavy metal resistance genes, chaperones and mannosylglycerate as compatible solute and has the genetic ability to respond to environmental changes by signal transduction via a large number of two-component systems, by chemotaxis and flagella-mediated motility and possibly even by gas vacuole formation. These findings extend our understanding of thaumarchaeal evolution and physiology and offer many testable hypotheses for future experimental research on these nitrifiers.
ESTHER : Spang_2012_Environ.Microbiol_14_3122
PubMedSearch : Spang_2012_Environ.Microbiol_14_3122
PubMedID: 23057602
Gene_locus related to this paper: nitgg-k0im51

Title : The metagenome-derived enzymes LipS and LipT increase the diversity of known lipases - Chow_2012_PLoS.One_7_e47665
Author(s) : Chow J , Kovacic F , Dall Antonia Y , Krauss U , Fersini F , Schmeisser C , Lauinger B , Bongen P , Pietruszka J , Schmidt M , Menyes I , Bornscheuer UT , Eckstein M , Thum O , Liese A , Mueller-Dieckmann J , Jaeger KE , Streit WR
Ref : PLoS ONE , 7 :e47665 , 2012
Abstract : Triacylglycerol lipases (EC 3.1.1.3) catalyze both hydrolysis and synthesis reactions with a broad spectrum of substrates rendering them especially suitable for many biotechnological applications. Most lipases used today originate from mesophilic organisms and are susceptible to thermal denaturation whereas only few possess high thermotolerance. Here, we report on the identification and characterization of two novel thermostable bacterial lipases identified by functional metagenomic screenings. Metagenomic libraries were constructed from enrichment cultures maintained at 65 to 75 degrees C and screened resulting in the identification of initially 10 clones with lipolytic activities. Subsequently, two ORFs were identified encoding lipases, LipS and LipT. Comparative sequence analyses suggested that both enzymes are members of novel lipase families. LipS is a 30.2 kDa protein and revealed a half-life of 48 h at 70 degrees C. The lipT gene encoded for a multimeric enzyme with a half-life of 3 h at 70 degrees C. LipS had an optimum temperature at 70 degrees C and LipT at 75 degrees C. Both enzymes catalyzed hydrolysis of long-chain (C(12) and C(14)) fatty acid esters and additionally hydrolyzed a number of industry-relevant substrates. LipS was highly specific for (R)-ibuprofen-phenyl ester with an enantiomeric excess (ee) of 99%. Furthermore, LipS was able to synthesize 1-propyl laurate and 1-tetradecyl myristate at 70 degrees C with rates similar to those of the lipase CalB from Candida antarctica. LipS represents the first example of a thermostable metagenome-derived lipase with significant synthesis activities. Its X-ray structure was solved with a resolution of 1.99 A revealing an unusually compact lid structure.
ESTHER : Chow_2012_PLoS.One_7_e47665
PubMedSearch : Chow_2012_PLoS.One_7_e47665
PubMedID: 23112831
Gene_locus related to this paper: symth-q67mr3 , 9bact-k7qe48

Title : Cloning, expression, purification and preliminary X-ray analysis of a putative metagenome-derived lipase - Fersini_2012_Acta.Crystallogr.Sect.F.Struct.Biol.Cryst.Commun_68_923
Author(s) : Fersini F , Dall'Antonia Y , Chow J , Streit WR , Mueller-Dieckmann J
Ref : Acta Crystallographica Sect F Struct Biol Cryst Commun , 68 :923 , 2012
Abstract : LipS is a novel thermostable putative lipase that was isolated from a metagenomic library using functional screening methods. The corresponding gene shows high similarity to that encoding a putative but uncharacterized esterase from Symbiobacterium thermophilum IAM14863 (99% nucleotide-sequence similarity). Two different constructs of the recombinant lipase were crystallized. Crystals belonging to space group P4(2)2(1)2 diffracted X-ray radiation to 2.8 A resolution and crystals belonging to space group P4 diffracted to 2.0 A resolution. The most probable content of their asymmetric units were two molecules (P4(2)2(1)2) and four or five molecules (P4), respectively.
ESTHER : Fersini_2012_Acta.Crystallogr.Sect.F.Struct.Biol.Cryst.Commun_68_923
PubMedSearch : Fersini_2012_Acta.Crystallogr.Sect.F.Struct.Biol.Cryst.Commun_68_923
PubMedID: 22869123
Gene_locus related to this paper: symth-q67mr3

Title : Harvesting of novel polyhydroxyalkanaote (PHA) synthase encoding genes from a soil metagenome library using phenotypic screening - Schallmey_2011_FEMS.Microbiol.Lett_321_150
Author(s) : Schallmey M , Ly A , Wang C , Meglei G , Voget S , Streit WR , Driscoll BT , Charles TC
Ref : FEMS Microbiology Letters , 321 :150 , 2011
Abstract : We previously reported the construction of metagenomic libraries in the IncP cosmid vector pRK7813, enabling heterologous expression of these broad-host-range libraries in multiple bacterial hosts. Expressing these libraries in Sinorhizobium meliloti, we have successfully complemented associated phenotypes of polyhydroxyalkanoate synthesis mutants. DNA sequence analysis of three clones indicates that the complementing genes are homologous to, but substantially different from, known polyhydroxyalkanaote synthase-encoding genes. Thus we have demonstrated the ability to isolate diverse genes for polyhydroxyalkanaote synthesis by functional complementation of defined mutants. Such genes might be of use in the engineering of more efficient systems for the industrial production of bioplastics. The use of functional complementation will also provide a vehicle to probe the genetics of polyhydroxyalkanaote metabolism and its relation to carbon availability in complex microbial assemblages.
ESTHER : Schallmey_2011_FEMS.Microbiol.Lett_321_150
PubMedSearch : Schallmey_2011_FEMS.Microbiol.Lett_321_150
PubMedID: 21631577
Gene_locus related to this paper: 9bact-a3rgw9

Title : Enantioselective kinetic resolution of phenylalkyl carboxylic acids using metagenome-derived esterases - Fernandez-Alvaro_2010_Microb.Biotechnol_3_59
Author(s) : Fernandez-Alvaro E , Kourist R , Winter J , Bottcher D , Liebeton K , Naumer C , Eck J , Leggewie C , Jaeger KE , Streit WR , Bornscheuer UT
Ref : Microb Biotechnol , 3 :59 , 2010
Abstract : Enantiomerically pure beta-arylalkyl carboxylic acids are important synthetic intermediates for the preparation of a wide range of compounds with biological and pharmacological activities. A library of 83 enzymes isolated from the metagenome was searched for activity in the hydrolysis of ethyl esters of three racemic phenylalkyl carboxylic acids by a microtiter plate-based screening using a pH-indicator assay. Out of these, 20 enzymes were found to be active and were subjected to analytical scale biocatalysis in order to determine their enantioselectivity. The most enantioselective and also enantiocomplementary biocatalysts were then used for preparative scale reactions. Thus, both enantiomers of each of the three phenylalkyl carboxylic acids studied could be obtained in excellent optical purity and high yields.
ESTHER : Fernandez-Alvaro_2010_Microb.Biotechnol_3_59
PubMedSearch : Fernandez-Alvaro_2010_Microb.Biotechnol_3_59
PubMedID: 21255306
Gene_locus related to this paper: 9bact-Est8.6Y9K

Title : Rhizobium sp. strain NGR234 possesses a remarkable number of secretion systems - Schmeisser_2009_Appl.Environ.Microbiol_75_4035
Author(s) : Schmeisser C , Liesegang H , Krysciak D , Bakkou N , Le Quere A , Wollherr A , Heinemeyer I , Morgenstern B , Pommerening-Roser A , Flores M , Palacios R , Brenner S , Gottschalk G , Schmitz RA , Broughton WJ , Perret X , Strittmatter AW , Streit WR
Ref : Applied Environmental Microbiology , 75 :4035 , 2009
Abstract : Rhizobium sp. strain NGR234 is a unique alphaproteobacterium (order Rhizobiales) that forms nitrogen-fixing nodules with more legumes than any other microsymbiont. We report here that the 3.93-Mbp chromosome (cNGR234) encodes most functions required for cellular growth. Few essential functions are encoded on the 2.43-Mbp megaplasmid (pNGR234b), and none are present on the second 0.54-Mbp symbiotic plasmid (pNGR234a). Among many striking features, the 6.9-Mbp genome encodes more different secretion systems than any other known rhizobia and probably most known bacteria. Altogether, 132 genes and proteins are linked to secretory processes. Secretion systems identified include general and export pathways, a twin arginine translocase secretion system, six type I transporter genes, one functional and one putative type III system, three type IV attachment systems, and two putative type IV conjugation pili. Type V and VI transporters were not identified, however. NGR234 also carries genes and regulatory networks linked to the metabolism of a wide range of aromatic and nonaromatic compounds. In this way, NGR234 can quickly adapt to changing environmental stimuli in soils, rhizospheres, and plants. Finally, NGR234 carries at least six loci linked to the quenching of quorum-sensing signals, as well as one gene (ngrI) that possibly encodes a novel type of autoinducer I molecule.
ESTHER : Schmeisser_2009_Appl.Environ.Microbiol_75_4035
PubMedSearch : Schmeisser_2009_Appl.Environ.Microbiol_75_4035
PubMedID: 19376903
Gene_locus related to this paper: rhime-R01391 , rhime-R02260 , rhime-R02478 , rhisn-c3kku8 , rhisn-c3kl46 , rhisn-c3kly5 , rhisn-c3klz9 , rhisn-c3kmf4 , rhisn-c3kmp5 , rhisn-c3knq1 , rhisn-c3krv5 , rhisn-c3mdb6 , rhisn-c3mee2 , rhisn-c3meq6 , rhisn-c3mev4 , rhisn-c3mgd2 , rhisn-c3mil7 , rhisn-c3miq5 , rhisn-q6w1e1 , sinmw-a6ugj8 , rhisn-c3km61 , rhisn-c3m991 , sinfn-c3m9f4 , sinfn-y4kf

Title : Isolation and biochemical characterization of two novel metagenome-derived esterases - Elend_2006_Appl.Environ.Microbiol_72_3637
Author(s) : Elend C , Schmeisser C , Leggewie C , Babiak P , Carballeira JD , Steele HL , Reymond JL , Jaeger KE , Streit WR
Ref : Applied Environmental Microbiology , 72 :3637 , 2006
Abstract : The metagenomes of uncultured microbial communities are rich sources for novel biocatalysts. In this study, esterase EstA3 was derived from a drinking water metagenome, and esterase EstCE1 was derived from a soil metagenome. Both esterases are approximately 380 amino acids in size and show similarity to beta-lactamases, indicating that they belong to family VIII of the lipases/esterases. EstA3 had a temperature optimum at 50 degrees C and a pH optimum at pH 9.0. It was remarkably active and very stable in the presence of solvents and over a wide temperature and pH range. It is active in a multimeric form and displayed a high level of activity against a wide range of substrates including one secondary ester, 7-[3-octylcarboxy-(3-hydroxy-3-methyl-butyloxy)]-coumarin, which is normally unreactive. EstCE1 was active in the monomeric form and had a temperature optimum at 47 degrees C and a pH optimum at pH 10. It exhibited the same level of stability as EstA3 over wide temperature and pH ranges and in the presence of dimethyl sulfoxide, isopropanol, and methanol. EstCE1 was highly enantioselective for (+)-menthylacetate. These enzymes display remarkable characteristics that cannot be related to the original environment from which they were derived. The high level of stability of these enzymes together with their unique substrate specificities make them highly useful for biotechnological applications.
ESTHER : Elend_2006_Appl.Environ.Microbiol_72_3637
PubMedSearch : Elend_2006_Appl.Environ.Microbiol_72_3637
PubMedID: 16672512

Title : An evolutionary hot spot: the pNGR234b replicon of Rhizobium sp. strain NGR234 - Streit_2004_J.Bacteriol_186_535
Author(s) : Streit WR , Schmitz RA , Perret X , Staehelin C , Deakin WJ , Raasch C , Liesegang H , Broughton WJ
Ref : Journal of Bacteriology , 186 :535 , 2004
Abstract : Rhizobium sp. strain NGR234 has an exceptionally broad host range and is able to nodulate more than 112 genera of legumes. Since the overall organization of the NGR234 genome is strikingly similar to that of the narrow-host-range symbiont Rhizobium meliloti strain 1021 (also known as Sinorhizobium meliloti), the obvious question is why are the spectra of hosts so different? Study of the early symbiotic genes of both bacteria (carried by the SymA plasmids) did not provide obvious answers. Yet, both rhizobia also possess second megaplasmids that bear, among many other genes, those that are involved in the synthesis of extracellular polysaccharides (EPSs). EPSs are involved in fine-tuning symbiotic interactions and thus may help answer the broad- versus narrow-host-range question. Accordingly, we sequenced two fragments (total, 594 kb) that encode 575 open reading frames (ORFs). Comparisons revealed 19 conserved gene clusters with high similarity to R. meliloti, suggesting that a minimum of 28% (158 ORFs) of the genetic information may have been acquired from a common ancestor. The largest conserved cluster carried the exo and exs genes and contained 31 ORFs. In addition, nine highly conserved regions with high similarity to Agrobacterium tumefaciens C58, Bradyrhizobium japonicum USDA110, and Mesorhizobium loti strain MAFF303099, as well as two conserved clusters that are highly homologous to similar regions in the plant pathogen Erwinia carotovora, were identified. Altogether, these findings suggest that >/==" BORDER="0">40% of the pNGR234b genes are not strain specific and were probably acquired from a wide variety of other microbes. The presence of 26 ORFs coding for transposases and site-specific integrases supports this contention. Surprisingly, several genes involved in the degradation of aromatic carbon sources and genes coding for a type IV pilus were also found.
ESTHER : Streit_2004_J.Bacteriol_186_535
PubMedSearch : Streit_2004_J.Bacteriol_186_535
PubMedID: 14702322
Gene_locus related to this paper: rhime-R01391 , rhisn-c3kku8 , rhisn-c3kl46 , rhisn-c3kly5 , rhisn-c3klz9 , rhisn-c3kmf4 , rhisn-c3kmp5 , rhisn-c3knq1 , rhisn-c3krv5 , rhisn-q6w1e1 , rhisn-q6w231 , rhisn-q6w256 , sinmw-a6ugj8 , rhisn-c3km61

Title : Prospecting for biocatalysts and drugs in the genomes of non-cultured microorganisms - Streit_2004_Curr.Opin.Biotechnol_15_285
Author(s) : Streit WR , Daniel R , Jaeger KE
Ref : Curr Opin Biotechnol , 15 :285 , 2004
Abstract : Modern biotechnology has a steadily increasing demand for vitamins, antibiotics and, in particular, novel biocatalysts for use in the production of flavors, agrochemicals, pharmaceuticals and high-value fine chemicals. Novel experimental approaches are being developed in attempts to identify such molecules. However, it is known that up to 99.8% of the microbes present in many environments are not readily culturable; hence, they cannot be exploited for biotechnology. The 'metagenome technology' offers a solution to this problem by developing culture-independent methods to isolate, clone and express environmental DNA. So far, metagenome-based approaches have led to the isolation of many novel biocatalysts and a variety of other molecules with a high potential for downstream applications.
ESTHER : Streit_2004_Curr.Opin.Biotechnol_15_285
PubMedSearch : Streit_2004_Curr.Opin.Biotechnol_15_285
PubMedID: 15296926

Title : Metagenome survey of biofilms in drinking-water networks - Schmeisser_2003_Appl.Environ.Microbiol_69_7298
Author(s) : Schmeisser C , Stockigt C , Raasch C , Wingender J , Timmis KN , Wenderoth DF , Flemming HC , Liesegang H , Schmitz RA , Jaeger KE , Streit WR
Ref : Applied Environmental Microbiology , 69 :7298 , 2003
Abstract : Most naturally occurring biofilms contain a vast majority of microorganisms which have not yet been cultured, and therefore we have little information on the genetic information content of these communities. Therefore, we initiated work to characterize the complex metagenome of model drinking water biofilms grown on rubber-coated valves by employing three different strategies. First, a sequence analysis of 650 16S rRNA clones indicated a high diversity within the biofilm communities, with the majority of the microbes being closely related to the Proteobacteria: Only a small fraction of the 16S rRNA sequences were highly similar to rRNA sequences from Actinobacteria, low-G+C gram-positives and the Cytophaga-Flavobacterium-Bacteroides group. Our second strategy included a snapshot genome sequencing approach. Homology searches in public databases with 5,000 random sequence clones from a small insert library resulted in the identification of 2,200 putative protein-coding sequences, of which 1,026 could be classified into functional groups. Similarity analyses indicated that significant fractions of the genes and proteins identified were highly similar to known proteins observed in the genera Rhizobium, Pseudomonas, and Escherichia: Finally, we report 144 kb of DNA sequence information from four selected cosmid clones, of which two formed a 75-kb overlapping contig. The majority of the proteins identified by whole-cosmid sequencing probably originated from microbes closely related to the alpha-, beta-, and gamma-Proteobacteria: The sequence information was used to set up a database containing the phylogenetic and genomic information on this model microbial community. Concerning the potential health risk of the microbial community studied, no DNA or protein sequences directly linked to pathogenic traits were identified.
ESTHER : Schmeisser_2003_Appl.Environ.Microbiol_69_7298
PubMedSearch : Schmeisser_2003_Appl.Environ.Microbiol_69_7298
PubMedID: 14660379
Gene_locus related to this paper: 9bact-q6wlc7

Title : Prospecting for novel biocatalysts in a soil metagenome - Voget_2003_Appl.Environ.Microbiol_69_6235
Author(s) : Voget S , Leggewie C , Uesbeck A , Raasch C , Jaeger KE , Streit WR
Ref : Applied Environmental Microbiology , 69 :6235 , 2003
Abstract : The metagenomes of complex microbial communities are rich sources of novel biocatalysts. We exploited the metagenome of a mixed microbial population for isolation of more than 15 different genes encoding novel biocatalysts by using a combined cultivation and direct cloning strategy. A 16S rRNA sequence analysis revealed the presence of hitherto uncultured microbes closely related to the genera Pseudomonas, Agrobacterium, Xanthomonas, Microbulbifer, and Janthinobacterium. Total genomic DNA from this bacterial community was used to construct cosmid DNA libraries, which were functionally searched for novel enzymes of biotechnological value. Our searches in combination with cosmid sequencing resulted in identification of four clones encoding 12 putative agarase genes, most of which were organized in clusters consisting of two or three genes. Interestingly, nine of these agarase genes probably originated from gene duplications. Furthermore, we identified by DNA sequencing several other biocatalyst-encoding genes, including genes encoding a putative stereoselective amidase (amiA), two cellulases (gnuB and uvs080), an alpha-amylase (amyA), a 1,4-alpha-glucan branching enzyme (amyB), and two pectate lyases (pelA and uvs119). Also, a conserved cluster of two lipase genes was identified, which was linked to genes encoding a type I secretion system. The novel gene aguB was overexpressed in Escherichia coli, and the enzyme activities were determined. Finally, we describe more than 162 kb of DNA sequence that provides a strong platform for further characterization of this microbial consortium.
ESTHER : Voget_2003_Appl.Environ.Microbiol_69_6235
PubMedSearch : Voget_2003_Appl.Environ.Microbiol_69_6235
PubMedID: 14532085
Gene_locus related to this paper: 9bact-q6xci1 , 9bact-q6xci2