1. Usmerjeno vzorčenje podtalnih in pitnih voda na aktivne snovi pesticidov in njihovih razgradnih produktov v letu 2024Primož Bukovec, Tanja Fatur, Žan Trošt, 2025, professional article Abstract: V okviru strokovne naloge smo spremljali vsebnost aktivnih snovi v FFS in njihovih razgradnih produktov v podzemnih vodah Slovenije. Na ostanke aktivnih snovi je bilo pregledanih 34 vzorcev podtalne vode in 7 vzorcev pitne vode, odvzetih na več lokacijah na treh območjih, in sicer v Savinjski kotlini (sedem odvzemnih mest), Dravski kotlini (sedem odvzemnih mest) in Murski kotlini (deset odvzemnih mest). Izbrana mesta za vzorčenje podtalnice so bila določena na podlagi hidrogeoloških in pedoloških značilnosti ter kmetijskih praks na posameznem območju. Ta mesta predstavljajo najbolj kritične točke za spiranje pesticidov v podzemno vodo, saj izpolnjujejo ključne kriterije, ki povečujejo tveganje za kontaminacijo. Vsak vzorec vode je bil analiziran na več kot 500 komponent fitofarmacevtskih sredstev (aktivne snovi in metaboliti). V vseh analiziranih vzorcih podtalne vode je bilo zaznanih 20 različnih aktivnih snovi oz. njihovih metabolitov, kar predstavlja okoli 3 % vseh analiziranih komponent. V vseh analiziranih vzorcih pitne vode pa je bilo zaznanih le 6 različnih komponent aktivnih snovi oz. njihovih metabolitov, kar predstavlja manj kot 1 % od vseh analiziranih komponent. Vzorčenje in analiza izbranih podtalnih in pitnih voda v delih Slovenije, kjer se izvaja najintenzivnejša kmetijska pridelava na najranljivejših tleh za spiranje v podtalnico, sta pokazala, da imamo na teh območjih kmetijske dejavnosti relativno malo ostankov aktivnih snovi. Raziskave na področju podzemnih voda se bodo nadaljevale in po potrebi bomo dodali v program še nove aktivne snovi in metabolite FFS.
Keywords: monitoring podzemnih voda, pesticidi, metaboliti, pitna voda, aktivne snovi v FFS
Published in DiRROS: 26.02.2026; Views: 400; Downloads: 310
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2. Roles of the crotonyl-CoA carboxylase/reductase homologues in acetate assimilation and biosynthesis of immunosuppressant FK506 in Streptomyces tsukubaensisGregor Kosec, Hrvoje Petković, Špela Baebler, Kristina Gruden, Marko Blažič, 2015, original scientific article Abstract: Background
In microorganisms lacking a functional glyoxylate cycle, acetate can be assimilated by alternative pathways of carbon metabolism such as the ethylmalonyl-CoA (EMC) pathway. Among the enzymes converting CoA-esters of the EMC pathway, there is a unique carboxylase that reductively carboxylates crotonyl-CoA, crotonyl-CoA carboxylase/reductase (Ccr). In addition to the EMC pathway, gene homologues of ccr can be found in secondary metabolite gene clusters that are involved in the provision of structurally diverse extender units used in the biosynthesis of polyketide natural products. The roles of multiple ccr homologues in the same genome and their potential interactions in primary and secondary metabolic pathways are poorly understood.
Results
In the genome of S. tsukubaensis we have identified two ccr homologues; ccr1 is located in the putative ethylmalonyl-CoA (emc) operon and allR is located on the left fringe of the FK506 cluster. AllR provides an unusual extender unit allylmalonyl-CoA (ALL) for the biosynthesis of FK506 and potentially also ethylmalonyl-CoA for the related compound FK520. We have demonstrated that in S. tsukubaensis the ccr1 gene does not have a significant role in the biosynthesis of FK506 or FK520 when cultivated on carbohydrate-based media. However, when overexpressed under the control of a strong constitutive promoter, ccr1 can take part in the biosynthesis of ethylmalonyl-CoA and thereby FK520, but not FK506. In contrast, if ccr1 is inactivated, allR is not able to sustain a functional ethylmalonyl-CoA pathway (EMC) and cannot support growth on acetate as the sole carbon source, even when constitutively expressed in the chimeric emc operon. This is somewhat surprising considering that the same chimeric emc operon results in production of FK506 as well as FK520, consistent with the previously proposed relaxed specificity of AllR for C4 and C5 substrates.
Conclusions
Different regulation of the expression of both ccr genes, ccr1 and allR, and their corresponding pathways EMC and ALL, respectively, in combination with the different enzymatic properties of the Ccr1 and AllR enzymes, determine an almost exclusive role of ccr1 in the EMC pathway in S. tsukubaensis, and an exclusive role of allR in the biosynthesis of FK506/FK520, thus separating the functional roles of these two genes between the primary and secondary metabolic pathways.
Keywords: streptomicete, Streptomyces tsukubaensis, sekundarni metaboliti, takrolimus, FK506, biosinteze poliketidov
Published in DiRROS: 29.07.2024; Views: 1589; Downloads: 823
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3. Integrated omics approaches provide strategies for rapid erythromycin yield increase in Saccharopolyspora erythraeaKatarina Karničar, Igor Drobnak, Marko Petek, Vasilka Magdevska, Jaka Horvat, Robert Vidmar, Špela Baebler, Ana Rotter, Polona Jamnik, Štefan Fujs, Boris Turk, Marko Fonović, Kristina Gruden, Gregor Kosec, Hrvoje Petković, 2016, original scientific article Abstract: Background
Omics approaches have significantly increased our understanding of biological systems. However, they have had limited success in explaining the dramatically increased productivity of commercially important natural products by industrial high-producing strains, such as the erythromycin-producing actinomycete Saccharopolyspora erythraea. Further yield increase is of great importance but requires a better understanding of the underlying physiological processes.
Results
To reveal the mechanisms related to erythromycin yield increase, we have undertaken an integrated study of the genomic, transcriptomic, and proteomic differences between the wild type strain NRRL2338 (WT) and the industrial high-producing strain ABE1441 (HP) of S. erythraea at multiple time points of a simulated industrial bioprocess. 165 observed mutations lead to differences in gene expression profiles and protein abundance between the two strains, which were most prominent in the initial stages of erythromycin production. Enzymes involved in erythromycin biosynthesis, metabolism of branched chain amino acids and proteolysis were most strongly upregulated in the HP strain. Interestingly, genes related to TCA cycle and DNA-repair were downregulated. Additionally, comprehensive data analysis uncovered significant correlations in expression profiles of the erythromycin-biosynthetic genes, other biosynthetic gene clusters and previously unidentified putative regulatory genes. Based on this information, we demonstrated that overexpression of several genes involved in amino acid metabolism can contribute to increased yield of erythromycin, confirming the validity of our systems biology approach.
Conclusions
Our comprehensive omics approach, carried out in industrially relevant conditions, enabled the identification of key pathways affecting erythromycin yield and suggests strategies for rapid increase in the production of secondary metabolites in industrial environment.
Keywords: aktinomicete, Saccharopolyspora erythraea, sekundarni metaboliti, antibiotiki, eritromicin, biosinteza, metabolno inženirstvo, proteomika
Published in DiRROS: 25.07.2024; Views: 1709; Downloads: 936
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4. Vpliv glivnih in rastlinskih sekundarnih metabolitov na verižno reakcijo s polimerazo (PCR)Nejc Thaler, Marko Bajc, 2013, review article Abstract: Sekundarni metaboliti so organske spojine, ki jih najdemo pri glivah in rastlinah, kjer imajo vlogo obrambnih in signalnih molekul ali zagotavljajo druge selekcijske prednosti, niso pa neposredno vpleteni v rast, razvoj in razmnoževanje organizma. Pri delu s tehnikami DNA so pogosto ravno sekundarni metaboliti tisti, ki posredno ali neposredno vplivajo na uspešnost verižne reakcije s polimerazo (PCR) ali reverezno transkriptazo, in sicer tako, da otežujejo celično lizo, povzročajo razpad nukleinskih kislin ali neposredno ovirajo delovanje encima polimeraze pri pomnoževanju tarčne DNK. Glavna ovira pri aplikaciji tehnike PCR v rutinski diagnostiki je priprava visoko kvalitetne DNA brez inhibitorjev. Še posebej to velja pri izolaciji DNA iz lesnatih rastlin (Minafra in sod., 1992) in vzorcev tal (Tsai in Olson, 1991). Večina standardnih postopkov izolacije nukleinskih kislin ne odstrani rastlinskih polisaharidov in polifenolnih komponent, ki imajo lahko neposreden vpliv na pomnoževanje s PCR (Demeke in Adams, 1992). Poskusi za premostitev tovrstnih ovir vključujejo bolj dovršene metode za izolacijo nukleinskih kislin in PCR, ki vključujejo uporabo pospeševalcev PCR za odstranitev ali zmanjšanje vpliva inhibitorjev PCR. Ta pregled je osredotočen na pristope za odstranitev ali zmanjšanje vplivov rastlinskih in glivnih sekundarnih metabolitov iz vzorcev tal, različnih rastlinskih tkiv in razkrojenega lesa zaradi pomena tovrstnih raziskav za gozdarstvo in lesarstvo.
Keywords: sekundarni metaboliti, izolacija DNA, pomnoževanje DNA, verižna reakcija, polimeraza, PCR
Published in DiRROS: 12.07.2017; Views: 6866; Downloads: 3044
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