1. Extremophilic microorganisms in Central EuropeVera Zgonik, Janez Mulec, Tina Eleršek, Nives Ogrinc, Polona Jamnik, Nataša Poklar Ulrih, 2021, review article Abstract: Extremophiles inhabit a wide variety of environments. Here we focus on extremophiles in moderate climates in central Europe, and particularly in Slovenia. Although multiple types of stress often occur in the same habitat, extremophiles are generally combined into groups according to the main stressor to which they are adapted. Several types of extremophiles, e.g., oligotrophs, are well represented and diverse in subsurface environments and karst regions. Psychrophiles thrive in ice caves and depressions with eternal snow and ice, with several globally distributed snow algae and psychrophilic bacteria that have been discovered in alpine glaciers. However, this area requires further research. Halophiles thrive in salterns while thermophiles inhabit thermal springs, although there is little data on such microorganisms in central Europe, despite many taxa being found globally. This review also includes the potential use of extremophiles in biotechnology and bioremediation applications.
Keywords: ekstremofilni mikroorganizmi, mikrobna ekologija, ekstremofili, oligotrofi, psihrofili, halofili, termofili
Published in DiRROS: 05.08.2024; Views: 53; Downloads: 79
 Full text (4,24 MB)
This document has many files! More... |
2. SACE_5599, a putative regulatory protein, is involved in morphological differentiation and erythromycin production in Saccharopolyspora erythraeaBenjamin Kirm, Vasilka Magdevska, Miha Tome, Marinka Horvat, Katarina Karničar, Marko Petek, Robert Vidmar, Špela Baebler, Polona Jamnik, Štefan Fujs, Jaka Horvat, Marko Fonović, Boris Turk, Kristina Gruden, Hrvoje Petković, Gregor Kosec, 2013, original scientific article Abstract: Background
Erythromycin is a medically important antibiotic, biosynthesized by the actinomycete Saccharopolyspora erythraea. Genes encoding erythromycin biosynthesis are organized in a gene cluster, spanning over 60 kbp of DNA. Most often, gene clusters encoding biosynthesis of secondary metabolites contain regulatory genes. In contrast, the erythromycin gene cluster does not contain regulatory genes and regulation of its biosynthesis has therefore remained poorly understood, which has for a long time limited genetic engineering approaches for erythromycin yield improvement.
Results
We used a comparative proteomic approach to screen for potential regulatory proteins involved in erythromycin biosynthesis. We have identified a putative regulatory protein SACE_5599 which shows significantly higher levels of expression in an erythromycin high-producing strain, compared to the wild type S. erythraea strain. SACE_5599 is a member of an uncharacterized family of putative regulatory genes, located in several actinomycete biosynthetic gene clusters. Importantly, increased expression of SACE_5599 was observed in the complex fermentation medium and at controlled bioprocess conditions, simulating a high-yield industrial fermentation process in the bioreactor. Inactivation of SACE_5599 in the high-producing strain significantly reduced erythromycin yield, in addition to drastically decreasing sporulation intensity of the SACE_5599-inactivated strains when cultivated on ABSM4 agar medium. In contrast, constitutive overexpression of SACE_5599 in the wild type NRRL23338 strain resulted in an increase of erythromycin yield by 32%. Similar yield increase was also observed when we overexpressed the bldD gene, a previously identified regulator of erythromycin biosynthesis, thereby for the first time revealing its potential for improving erythromycin biosynthesis.
Conclusions
SACE_5599 is the second putative regulatory gene to be identified in S. erythraea which has positive influence on erythromycin yield. Like bldD, SACE_5599 is involved in morphological development of S. erythraea, suggesting a very close relationship between secondary metabolite biosynthesis and morphological differentiation in this organism. While the mode of action of SACE_5599 remains to be elucidated, the manipulation of this gene clearly shows potential for improvement of erythromycin production in S. erythraea in industrial setting. We have also demonstrated the applicability of the comparative proteomics approach for identifying new regulatory elements involved in biosynthesis of secondary metabolites in industrial conditions.
Keywords: erythromycin, polyketide, regulator, SACE_5599, lmbU, differentiation (biology), sporulation, strain improvement, metabolic engineering
Published in DiRROS: 02.08.2024; Views: 87; Downloads: 92
Full text (1,18 MB)
This document has many files! More... |
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: 133; Downloads: 106
Full text (3,06 MB)
This document has many files! More... |
4. The role of luxS in Campylobacter jejuni beyond intercellular signalingDina Jug, Blaž Jug, Katarina Šimunović, Magda Tušek-Žnidarič, Urban Kunej, Nataša Toplak, Minka Kovač, Marjorie Fournier, Polona Jamnik, Sonja Smole Možina, Anja Klančnik, 2023, original scientific article Keywords: Campylobacter jejuni, luxS, intercellular signaling, transcriptome, proteome, metabolism, stress response
Published in DiRROS: 12.07.2024; Views: 117; Downloads: 110
Full text (4,54 MB)
This document has many files! More... |
