The environmental hazard posed by the accumulation of huge amounts of used tires might be partly relieved by the implementation of methods for recycling natural rubber (NR) from waste tires. This approach requires rubber grinding and a process of devulcanization that breaks the sulfur-sulfur crosslinks among polymer chains. Several chemic al or mechanical methods are already used to devulcanize ground-rubber. However, each of them has drawbacks related either to the lack of specificity or to the use of hazardous chemicals. It would therefore be desirable to develop processes in which selective and specific reactions are carried out in mild conditions of temperature and pressure, without the use of hazardous compounds. In this view, the use of biocatalysts could be a valuable and ecological alternative. This study explores the possibility of applying enzymes to devulcanize rubber in a process of “biodevulcanization”. Since enzymes active in rubber devulcanization were not available at the beginning of this thesis, this research started with the analysis of microorganisms isolated from environmental samples contaminated with waste tires. The desulfuring properties of several bacteria were tested on the model substrate dibenzothiophene (DBT). A first in-vivo screening of microorganisms allowed the selection of a new strain of Rhodococcus sp. referred as AF21875. This microorganism was studied with two aims: assessing the presence of a metabolic pathway for DBT desulfurization already described in other bacteria and identifying new metabolic abilities and enzymes. In bacteria active in desulfurization, four enzymes co-operate in the reaction of desulfurization: DszA, DszB, DszC and DszD. The presence of the four corresponding dsz genes in the genomic DNA of Rhodococcus sp. AF21875 has been assessed. The four genes have been cloned in a strain of the bacterium Escherichia coli to allow for the production of recombinant Dsz enzymes. The three recombinant proteins DszA, DszC and DszD are soluble and were successfully purified. More difficult was the production of DszB that is poorly expressed in any experimental condition. In view of a biotechnological application, structural and stability studies were carried out on DszA, DszC and DszD enzymes. In particular, we investigated secondary structure and heat stability by circular dichroism, while protein stability in the presence of different organic solvents was studied by spectrofluorimetry. Enzymes activity on DBT was assessed by high performance liquid chromatography (HPLC) by detecting the formation of 2 -hydroxybiphenyl (HBP), the reaction product of DBT desulfurization. The desulfurization activity of the four enzymes was then tested on vulcanized natural rubber using Rubber Process Analyzer and Fourier Transform Infrared Spectroscopy to detect chemical modifications induced by the enzymatic treatment. These analyses revealed minor changes. Other studies should be performed to attribute such modifications to desulfurization. Overall, Dsz enzymes from Rhodococcus sp. AF21875 were found to be an interesting starting point for the application of protein engineering approaches aimed to improve not only their activity but also their stability. A differential proteomic analysis of Rhodococcus sp. AF21875 was performed to identify enzymatic activities related to sulfur metabolism and different from Dsz proteins. Total proteins, extracted from cells grown either in the presence or in the absence of DBT, were separated by two-dimensional electrophoresis, showing that DBT induces a few changes in the proteome of Rhodococcus sp. AF21875. Three proteins, belonging to a metabolic pathway different from the Dsz one were identified by in-gel tryptic digestion and mass spectrometry.

L’enorme quantità di pneumatici fuori uso accumulati costituisce un grave problema ambientale. Per porvi rimedio si cercano soluzioni che mirano al riutilizzo della gomma naturale (NR), principale materia prima utilizzata nella produzione di pneumatici. Per poter essere riutilizzata, la NR viene generalmente macinata finemente e sottoposta ad un trattamento di devulcanizzazione, cioè alla rottura dei ponti trasversali zolfo-zolfo. Diversi metodi chimici o meccanici sono utilizzabili per devulcanizzare il polverino. Tuttavia, ciascuno di essi presenta degli svantaggi. Sarebbe quindi auspicabile la messa a punto di processi in cui reazioni specifiche siano realizzate in condizioni moderate di temperatura e pressione. In questo scenario l’utilizzo di biocatalizzatori potrebbe costituire un’alternativa valida e di minor impatto ambientale. Questo studio si occupa di verificare la possibilità di trattamenti enzimatici di “biodevulcanizzazione”. Non essendo noti enzimi in grado di devulcanizzare la gomma, questo lavoro di tesi è partito dall’analisi di microrganismi isolati da campioni ambientali e con potenziali proprietà desolforanti che sono state saggiate su un substrato modello, il dibenzotiofene (DBT). Il primo screening sui microrganismi ha portato alla selezione di un nuovo ceppo di Rhodococcus sp. AF21875. L’attività desolforante di questo microrganismo è stata studiata con due approcci paralleli, da un lato verificando la presenza di geni codificanti per enzimi che desolforano il DBT e dall’altro individuando nuovi enzimi con abilità desolforanti. In batteri attivi in processi di desolforazione, i geni dsz codificano per 4 enzimi: DszA, DszB, DszC e DszD. Nel DNA genomico di Rhodococcus sp. AF21875 è stata verificata la presenza dei quattro geni dsz, che sono stati clonati per consentire la produzione ricombinante delle proteine corrispondenti in un ceppo del batterio Escherichia coli. Tre delle proteine, DszA, DszC e DszD, sono abbondantemente espresse in forma solubile e sono state purificate con successo. In previsione di un impiego biotecnologico delle proteine DszA, DszC e DszD è stata intrapresa l’analisi di alcune caratteristiche strutturali e di stabilità. In particolare, è stata analizzata la composizione della struttura secondaria e la stabilità al calore mediante dicroismo circolare; la stabilità in presenza di diversi solventi organici, attraverso spettrofluorimetria. L’attività degli enzimi è stata monitorata mediante cromatografia liquida (HPLC) che consente di rilevare la formazione di 2-idrossibifenile (HBP) come prodotto finale di reazione. L’attività di desolforazione dei quattro enzimi è stata infine saggiata su gomma naturale vulcanizzata. È emerso che il trattamento enzimatico provoca modificazioni chimiche della gomma. Sebbene le analisi condotte evidenzino cambiamenti di modesta entità e non associabili univocamente ad un processo di desolforazione, gli enzimi individuati costituiscono un buon punto di partenza per approcci di ingegneria proteica volti a migliorare l’attività e la stabilità degli enzimi Dsz da Rhodococcus sp. AF21875. Inoltre, per individuare nuove attività enzimatiche è stata eseguita un’analisi di proteomica differenziale delle cellule di Rhodococcus sp. AF21875. Da cellule cresciute in terreno privo o addizionato di DBT sono state estratte le proteine totali che sono state analizzate mediante elettroforesi bidimensionale. Quando Rhodococcus sp. AF21875 cresce in presenza di DBT, produce un pool di proteine che non si ritrovano tra le proteine espresse in assenza di DBT. Tre delle proteine sono state analizzate tramite digestione triptica in gel e analisi di spettrometria di massa. Questa analisi ha permesso di identificare due enzimi che non sono coinvolti nel metabolismo dello zolfo ma appartengono ad una stessa via catabolica distinta da quella cui appartengono gli enzimi Dsz.

(2015). Characterization of enzymes from desulfurizing bacterial strains. (Tesi di dottorato, Università degli Studi di Milano-Bicocca, 2015).

Characterization of enzymes from desulfurizing bacterial strains

PARRAVICINI, FEDERICA
2015

Abstract

The environmental hazard posed by the accumulation of huge amounts of used tires might be partly relieved by the implementation of methods for recycling natural rubber (NR) from waste tires. This approach requires rubber grinding and a process of devulcanization that breaks the sulfur-sulfur crosslinks among polymer chains. Several chemic al or mechanical methods are already used to devulcanize ground-rubber. However, each of them has drawbacks related either to the lack of specificity or to the use of hazardous chemicals. It would therefore be desirable to develop processes in which selective and specific reactions are carried out in mild conditions of temperature and pressure, without the use of hazardous compounds. In this view, the use of biocatalysts could be a valuable and ecological alternative. This study explores the possibility of applying enzymes to devulcanize rubber in a process of “biodevulcanization”. Since enzymes active in rubber devulcanization were not available at the beginning of this thesis, this research started with the analysis of microorganisms isolated from environmental samples contaminated with waste tires. The desulfuring properties of several bacteria were tested on the model substrate dibenzothiophene (DBT). A first in-vivo screening of microorganisms allowed the selection of a new strain of Rhodococcus sp. referred as AF21875. This microorganism was studied with two aims: assessing the presence of a metabolic pathway for DBT desulfurization already described in other bacteria and identifying new metabolic abilities and enzymes. In bacteria active in desulfurization, four enzymes co-operate in the reaction of desulfurization: DszA, DszB, DszC and DszD. The presence of the four corresponding dsz genes in the genomic DNA of Rhodococcus sp. AF21875 has been assessed. The four genes have been cloned in a strain of the bacterium Escherichia coli to allow for the production of recombinant Dsz enzymes. The three recombinant proteins DszA, DszC and DszD are soluble and were successfully purified. More difficult was the production of DszB that is poorly expressed in any experimental condition. In view of a biotechnological application, structural and stability studies were carried out on DszA, DszC and DszD enzymes. In particular, we investigated secondary structure and heat stability by circular dichroism, while protein stability in the presence of different organic solvents was studied by spectrofluorimetry. Enzymes activity on DBT was assessed by high performance liquid chromatography (HPLC) by detecting the formation of 2 -hydroxybiphenyl (HBP), the reaction product of DBT desulfurization. The desulfurization activity of the four enzymes was then tested on vulcanized natural rubber using Rubber Process Analyzer and Fourier Transform Infrared Spectroscopy to detect chemical modifications induced by the enzymatic treatment. These analyses revealed minor changes. Other studies should be performed to attribute such modifications to desulfurization. Overall, Dsz enzymes from Rhodococcus sp. AF21875 were found to be an interesting starting point for the application of protein engineering approaches aimed to improve not only their activity but also their stability. A differential proteomic analysis of Rhodococcus sp. AF21875 was performed to identify enzymatic activities related to sulfur metabolism and different from Dsz proteins. Total proteins, extracted from cells grown either in the presence or in the absence of DBT, were separated by two-dimensional electrophoresis, showing that DBT induces a few changes in the proteome of Rhodococcus sp. AF21875. Three proteins, belonging to a metabolic pathway different from the Dsz one were identified by in-gel tryptic digestion and mass spectrometry.
LOTTI, MARINA
Desulfurization, Biodesulfurization, dsz enzymes, 4S pathway
BIO/10 - BIOCHIMICA
English
2-mar-2015
Scuola di dottorato di Scienze
SCIENZA DEI MATERIALI - 08R
27
2013/2014
open
(2015). Characterization of enzymes from desulfurizing bacterial strains. (Tesi di dottorato, Università degli Studi di Milano-Bicocca, 2015).
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10281/76247
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