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  1. Article ; Online: Recent Insights into Escherichia coli and Vibrio spp. Pathogenicity and Responses to Stress

    Vladimir R. Kaberdin / Inés Arana

    Microorganisms, Vol 10, Iss 38, p

    2022  Volume 38

    Abstract: The ubiquitous presence of microorganisms is largely attributed to their tremendous capacity to successfully adapt and survive in highly adverse environments [.] ...

    Abstract The ubiquitous presence of microorganisms is largely attributed to their tremendous capacity to successfully adapt and survive in highly adverse environments [.]
    Keywords n/a ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2022-12-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: The Effect of Visible Light on Cell Envelope Subproteome during Vibrio harveyi Survival at 20 °C in Seawater

    Maite Orruño / Claudia Parada / Vladimir R. Kaberdin / Inés Arana

    Microorganisms, Vol 9, Iss 594, p

    2021  Volume 594

    Abstract: A number of Vibrio spp. belong to the well-studied model organisms used to understand the strategies developed by marine bacteria to cope with adverse conditions (starvation, suboptimal temperature, solar radiation, etc.) in their natural environments. ... ...

    Abstract A number of Vibrio spp. belong to the well-studied model organisms used to understand the strategies developed by marine bacteria to cope with adverse conditions (starvation, suboptimal temperature, solar radiation, etc.) in their natural environments. Temperature and nutrient availability are considered to be the key factors that influence Vibrio harveyi physiology, morphology, and persistence in aquatic systems. In contrast to the well-studied effects of temperature and starvation on Vibrio survival, little is known about the impact of visible light able to cause photooxidative stress. Here we employ V. harveyi ATCC 14126 T as a model organism to analyze and compare the survival patterns and changes in the protein composition of its cell envelope during the long-term permanence of this bacterium in seawater microcosm at 20 °C in the presence and absence of illumination with visible light. We found that V. harveyi exposure to visible light reduces cell culturability likely inducing the entry into the Viable but Non Culturable state (VBNC), whereas populations maintained in darkness remained culturable for at least 21 days. Despite these differences, the starved cells in both populations underwent morphological changes by reducing their size. Moreover, further proteomic analysis revealed a number of changes in the composition of cell envelope potentially accountable for the different adaptation pattern manifested in the absence and presence of visible light.
    Keywords Vibrio ; seawater ; starvation ; visible light ; membrane subproteome ; Biology (General) ; QH301-705.5
    Subject code 580
    Language English
    Publishing date 2021-03-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Combined Transcriptomic and Proteomic Profiling of E. coli under Microaerobic versus Aerobic Conditions

    Gunn-Guang Liou / Anna Chao Kaberdina / Wei-Syuan Wang / Vladimir R. Kaberdin / Sue Lin-Chao

    International Journal of Molecular Sciences, Vol 23, Iss 2570, p

    The Multifaceted Roles of Noncoding Small RNAs and Oxygen-Dependent Sensing in Global Gene Expression Control

    2022  Volume 2570

    Abstract: Adaptive mechanisms that facilitate intestinal colonization by the human microbiota, including Escherichia coli , may be better understood by analyzing the physiology and gene expression of bacteria in low-oxygen environments. We used high-throughput ... ...

    Abstract Adaptive mechanisms that facilitate intestinal colonization by the human microbiota, including Escherichia coli , may be better understood by analyzing the physiology and gene expression of bacteria in low-oxygen environments. We used high-throughput transcriptomics and proteomics to compare the expression profiles of E. coli grown under aerobic versus microaerobic conditions. Clustering of high-abundance transcripts under microaerobiosis highlighted genes controlling acid-stress adaptation ( gadAXW , gadAB , hdeAB-yhiD and hdeD operons), cell adhesion/biofilm formation ( pgaABCD and csgDEFG operons), electron transport ( cydAB ), oligopeptide transport ( oppABCDF ), and anaerobic respiration/fermentation ( hyaABCDEF and hycABCDEFGHI operons). In contrast, downregulated genes were involved in iron transport ( fhuABCD , feoABC and fepA-entD operons), iron-sulfur cluster assembly ( iscRSUA and sufABCDSE operons), aerobic respiration ( sdhDAB and sucABCDSE operons), and de novo nucleotide synthesis ( nrdHIEF ). Additionally, quantitative proteomics showed that the products (proteins) of these high- or low-abundance transcripts were expressed consistently. Our findings highlight interrelationships among energy production, carbon metabolism, and iron homeostasis. Moreover, we have identified and validated a subset of differentially expressed noncoding small RNAs (i.e., CsrC, RyhB, RprA and GcvB), and we discuss their regulatory functions during microaerobic growth. Collectively, we reveal key changes in gene expression at the transcriptional and post-transcriptional levels that sustain E. coli growth when oxygen levels are low.
    Keywords transcriptional and post-transcriptional regulation ; iron homeostasis ; anaerobic respiration ; acid stress response ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 570
    Language English
    Publishing date 2022-02-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article: Isolation of Pseudomonas fluorescens species highly resistant to pentachlorobenzene

    Montánchez, Itxaso / Anna Chao Kaberdina / Elena Sevillano / Lucía Gallego / Susana Rodríguez-Couto / Vladimir R. Kaberdin

    Folia microbiologica. 2017 July, v. 62, no. 4

    2017  

    Abstract: Polychlorinated aromatic compounds, including pentachlorobenzenes and hexachlorobenzenes, are recalcitrant industrial pollutants that cause adverse effects on living cells. In this paper, the isolation of Pseudomonas fluorescens species with high ... ...

    Abstract Polychlorinated aromatic compounds, including pentachlorobenzenes and hexachlorobenzenes, are recalcitrant industrial pollutants that cause adverse effects on living cells. In this paper, the isolation of Pseudomonas fluorescens species with high resistance to pentachlorobenzene (PeCB) is reported. It was found that, in contrast to its slightly negative effect on P. fluorescens growth, PeCB readily inhibited the cell growth of Serratia spp. and Escherichia coli strains, thus indicating that inhibition of bacterial growth by PeCB is species-dependent. Analysis of a P. fluorescens isolate revealed that the exposure to PeCB induced production of reactive oxygen species and led to an increase in the level of alkyl hydroperoxide reductase C (AhpC), an important enzyme enhancing the cell tolerance to organic hydroperoxides usually accumulated under oxidative stress. The putative mechanism conferring PeCB resistance to P. fluorescens and the potential use of P. fluorescens in bioremediation are discussed.
    Keywords Escherichia coli ; Pseudomonas fluorescens ; Serratia ; adverse effects ; aromatic compounds ; biological resistance ; bioremediation ; hydroperoxides ; microbial growth ; oxidative stress ; pollutants
    Language English
    Dates of publication 2017-07
    Size p. 325-334.
    Publishing place Springer Netherlands
    Document type Article
    ZDB-ID 240503-9
    ISSN 1874-9356 ; 0015-5632
    ISSN (online) 1874-9356
    ISSN 0015-5632
    DOI 10.1007/s12223-017-0501-3
    Database NAL-Catalogue (AGRICOLA)

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  5. Article ; Online: Towards new antituberculotic targets

    Agnes Csanadi / Mirijam-Elisabeth Zeller / Andras Miczak / Thierry Rose / Thierry Bizebard / Vladimir R. Kaberdin

    European Respiratory Review, Vol 17, Iss 108, Pp 76-

    biochemical characterisation of mycobacterial RNase E/G

    2008  Volume 77

    Abstract: The World Health Organization estimates that each year 3 million people die from tuberculosis (TB) and 8 million people become infected. No new anti-TB drugs have been introduced in the past 30 years, even though their development becomes increasingly ... ...

    Abstract The World Health Organization estimates that each year 3 million people die from tuberculosis (TB) and 8 million people become infected. No new anti-TB drugs have been introduced in the past 30 years, even though their development becomes increasingly important to face new challenges posed by multidrug-resistant and extensively drug-resistant strains and by acute infection with M. tuberculosis of HIV positive patients. Owing to its apparently important role in RNA metabolism, the RNase E/G family of endoribonucleases can be considered as a promising target for antimicrobial drugs. This consideration promted us to characterise biochemical properties of the M. tuberculosis RNase E/G homologue. To learn more about specific properties of RNase E/G homologues a M. tuberculosis RNase E/G (MycRne) was overexpressed in E. coli and purified as a 6His-tagged polypeptide. To characterise MycRne, we used in vitro cleavage assays and primer extension analysis of total RNA extracted from mycobacteria. We show that affinity purified MycRne has an endoribonucleolytic activity, which is dependent on the 5'-phosphorylation status of RNA. We could also show that RNase E/G has Mg2+ dependent activity and similar to E. coli RNase E, MycRne was able to cleave in an intercistronic region of the putative 9S precursor of 5S rRNA. Although, similar to E. coli RNase E, the mycobacterial RNase E/G homologue plays a role in rRNA processing, the substrate specificities of these enzymes show differences. This suggests that RNase E/G can be used as a promising target for antimicrobial drugs that can be optimized to specifically target pathogenic species.
    Keywords Diseases of the respiratory system ; RC705-779 ; Specialties of internal medicine ; RC581-951 ; Internal medicine ; RC31-1245 ; Medicine ; R ; DOAJ:Internal medicine ; DOAJ:Medicine (General) ; DOAJ:Health Sciences
    Language English
    Publishing date 2008-06-01T00:00:00Z
    Publisher European Respiratory Society
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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