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Shedding light on adhesion and biofilms of Halobacterium salinarum R1

Losensky, Gerald (2016)
Shedding light on adhesion and biofilms of Halobacterium salinarum R1.
Technische Universität Darmstadt
Dissertation, Erstveröffentlichung

Kurzbeschreibung (Abstract)

Biofilms, i.e. multicellular microbial communities, are widely accepted as the predominating mode of prokaryotes living in nature. However, knowledge about this lifestyle is still limited, especially in Archaea. The present work focuses on the formation of archaeal biofilms by the extremely halophilic archaeon Halobacterium salinarum R1.

Surface adhesion of Hbt. salinarum R1 was monitored by phase contrast microscopy and quantified in a fluorescence-based adhesion assay, and demonstrated that abiotic surfaces were successively colonized by the cells. The formation of complex three-dimensional cell clusters with tower-like structures up to 25 µm in height was observed within 15 days by scanning electron microscopy and confocal laser scanning microscopy. Extracellular polymeric substances, i.e. a complex biofilm matrix containing extracellular DNA and glycosidic residues, was detected using suitable molecular probes, as well as a high viability of the biofilm cells. The sequence of events observed during the biofilm formation consisted of adhesion, accumulation and maturation. Adherent cells contained different types of cell surface structures, since filaments with two predominant diameters (7-8 and 10 nm) were observed. One of the diameters belongs to the archaellum, whereas the smaller one belongs to pili involved in adhesion. The Hbt. salinarum R1 genome was searched for genes potentially associated with the synthesis of cell surface structures by bioinformatical analyses. Two gene loci, pil-1 and pil-2, putatively encoding type IV pilus-like structures were identified. It was demonstrated by RT-PCR that both loci were transciptionally active and cotranscribed. Moreover, qRT-PCR yielded 5.2- and 8.5-fold induction of the respective ATPase genes, pilB1 and pilB2, in adherent cells compared to planktonic cells. Deletion of the archaella ATPase gene, flaI, resulted in cells lacking the 10 nm filaments. These cells were non-motile but still showed the 7-8 nm appendages and strong adhesion. An additional deletion of pilB1 in a ΔflaI/ΔpilB1 mutant severely impaired the ability of the cells to adhere, which was reduced to 20% compared to the parental strain. In contrast, an additional deletion of pilB2 did not have further effects on adhesion. A search for genes encoding the filament subunits, i.e. pilins, yielded more than 30 candidates. Transcriptional analyses of the most likely candidates demonstrated differential expression of the genes in planktonic and adherent samples, with the genes pilA5, pilA6 and pilA7 showing 2.5- to 7.1-fold induction in initial biofilms. A proteome analysis of the biofilm formation was performed investigating planktonic as well as initial and mature biofilm cells of Hbt. salinarum R1. A molecular differentiation of the protein pattern was already observed by SDS-PAGE in samples derived from biofilms after one day compared to planktonic cells. Employing label-free mass spectrometric SWATH-LC/MS/MS analysis a high coverage of the predicted proteome was achieved, reflected by 1629 different proteins identified and 1464 proteins quantified (63.2% and 56.8% of the total proteome, respectively). A relative quantification was performed, showing between 55 and 245 proteins strongly altered (> 2-fold) when two of the cellular states were compared. 882 proteins showed statistically significant abundance changes, correspoding to 60.8% of the quantified proteins and 34.2% of the total proteome, respectivly, reflecting the high diversity of the processes affected. The relative changes detected ranged between 195-fold increase of an uncharacterized glutamine-rich alkaline protein (OE3542R) and 22.8-fold decrease of ribonucleoside-diphosphate reductase subunit beta (NrdB1). The most striking effects were observed with proteins involved in energy conversion, as well as proteins acting in nucleotide-, amino acid- and lipid metabolism. In addition, proteins associated with protein biosynthesis and cellular processes like cell motility and signal transduction were strongly affected. The proteomic data of selected proteins was validated by qRT-PCR transcriptional analyses.

This work represents the first comprehensive description of haloarchaeal biofilm formation using the example of Hbt. salinarum R1.

Typ des Eintrags: Dissertation
Erschienen: 2016
Autor(en): Losensky, Gerald
Art des Eintrags: Erstveröffentlichung
Titel: Shedding light on adhesion and biofilms of Halobacterium salinarum R1
Sprache: Englisch
Referenten: Pfeifer, Prof. Dr. Felicitas ; Kletzin, PD Dr. Arnulf
Publikationsjahr: 12 Mai 2016
Ort: Darmstadt
Datum der mündlichen Prüfung: 11 Juli 2016
URL / URN: http://tuprints.ulb.tu-darmstadt.de/5583
Kurzbeschreibung (Abstract):

Biofilms, i.e. multicellular microbial communities, are widely accepted as the predominating mode of prokaryotes living in nature. However, knowledge about this lifestyle is still limited, especially in Archaea. The present work focuses on the formation of archaeal biofilms by the extremely halophilic archaeon Halobacterium salinarum R1.

Surface adhesion of Hbt. salinarum R1 was monitored by phase contrast microscopy and quantified in a fluorescence-based adhesion assay, and demonstrated that abiotic surfaces were successively colonized by the cells. The formation of complex three-dimensional cell clusters with tower-like structures up to 25 µm in height was observed within 15 days by scanning electron microscopy and confocal laser scanning microscopy. Extracellular polymeric substances, i.e. a complex biofilm matrix containing extracellular DNA and glycosidic residues, was detected using suitable molecular probes, as well as a high viability of the biofilm cells. The sequence of events observed during the biofilm formation consisted of adhesion, accumulation and maturation. Adherent cells contained different types of cell surface structures, since filaments with two predominant diameters (7-8 and 10 nm) were observed. One of the diameters belongs to the archaellum, whereas the smaller one belongs to pili involved in adhesion. The Hbt. salinarum R1 genome was searched for genes potentially associated with the synthesis of cell surface structures by bioinformatical analyses. Two gene loci, pil-1 and pil-2, putatively encoding type IV pilus-like structures were identified. It was demonstrated by RT-PCR that both loci were transciptionally active and cotranscribed. Moreover, qRT-PCR yielded 5.2- and 8.5-fold induction of the respective ATPase genes, pilB1 and pilB2, in adherent cells compared to planktonic cells. Deletion of the archaella ATPase gene, flaI, resulted in cells lacking the 10 nm filaments. These cells were non-motile but still showed the 7-8 nm appendages and strong adhesion. An additional deletion of pilB1 in a ΔflaI/ΔpilB1 mutant severely impaired the ability of the cells to adhere, which was reduced to 20% compared to the parental strain. In contrast, an additional deletion of pilB2 did not have further effects on adhesion. A search for genes encoding the filament subunits, i.e. pilins, yielded more than 30 candidates. Transcriptional analyses of the most likely candidates demonstrated differential expression of the genes in planktonic and adherent samples, with the genes pilA5, pilA6 and pilA7 showing 2.5- to 7.1-fold induction in initial biofilms. A proteome analysis of the biofilm formation was performed investigating planktonic as well as initial and mature biofilm cells of Hbt. salinarum R1. A molecular differentiation of the protein pattern was already observed by SDS-PAGE in samples derived from biofilms after one day compared to planktonic cells. Employing label-free mass spectrometric SWATH-LC/MS/MS analysis a high coverage of the predicted proteome was achieved, reflected by 1629 different proteins identified and 1464 proteins quantified (63.2% and 56.8% of the total proteome, respectively). A relative quantification was performed, showing between 55 and 245 proteins strongly altered (> 2-fold) when two of the cellular states were compared. 882 proteins showed statistically significant abundance changes, correspoding to 60.8% of the quantified proteins and 34.2% of the total proteome, respectivly, reflecting the high diversity of the processes affected. The relative changes detected ranged between 195-fold increase of an uncharacterized glutamine-rich alkaline protein (OE3542R) and 22.8-fold decrease of ribonucleoside-diphosphate reductase subunit beta (NrdB1). The most striking effects were observed with proteins involved in energy conversion, as well as proteins acting in nucleotide-, amino acid- and lipid metabolism. In addition, proteins associated with protein biosynthesis and cellular processes like cell motility and signal transduction were strongly affected. The proteomic data of selected proteins was validated by qRT-PCR transcriptional analyses.

This work represents the first comprehensive description of haloarchaeal biofilm formation using the example of Hbt. salinarum R1.

Alternatives oder übersetztes Abstract:
Alternatives AbstractSprache

Biofilme, d.h. vielzellige mikrobielle Gemeinschaften, werden als die vorherrschende Lebensweise von Prokaryoten in der Natur angesehen. Dennoch sind die Kenntnisse über diese Lebensweise begrenzt, vor allem in der Domäne Archaea. Die vorliegende Arbeit beschäftigt sich mit der Bildung archaeeller Biofilme des extrem halophilen Archaeons Halobacterium salinarum R1. Oberflächenadhäsion von Hbt. salinarum R1 wurde durch Phasenkontrastmikroskopie beobachtet und mittels eines fluoreszenzbasierten Adhäsionsassays quantifiziert. Dabei zeigte sich eine sukzessive Kolonisierung abiotischer Oberflächen durch die Zellen. Unter Verwendung von Scanning Elektronenmikroskopie und Konfokaler Laser Scanning Mikroskopie, wurde innerhalb von 15 Tagen die Bildung komplexer dreidimensionaler Zellansammlungen einer Höhe von bis zu 25 µm beobachtet. Eine komplexe Biofilmmatrix aus extrazellulären polymeren Substanzen, wie extrazelluläre DNA und glykosidische Bestandteile, wurde mit geeigneten molekularen Sonden nachgewiesen, ebenso wie eine hohe Viabilität der Biofilmzellen. Der zeitliche Ablauf der Biofilmbildung setzte sich zusammen aus Adhäsion, Akkumulation und Reifung. Adhärente Zellen wiesen zwei verschiedene Typen von Zelloberflächenstrukturen auf, mit Durchmessern von 7-8 und 10 nm. Ein Typus stellte das Archaellum dar, während es sich bei dem dünneren Typus um Pili, welche in die Adhäsion involviert sind, handelte. Eine bioinformatische Suche nach potentiellen Genen, welche mit der Bildung von Zelloberflächenstrukturen assoziiert sind, im Genom von Hbt. salinarum R1, identifizierte zwei Genorte (pil-1 und pil-2), bei denen es sich um Typ IV Pili Systeme handelte. Mittels RT-PCR wurde gezeigt, dass beide Genorte transkriptionell aktiv waren und co-transkribiert wurden. Zudem ergab eine qRT-PCR-Analyse eine 5,2- bzw. 8,5-fache Induktion der jeweiligen ATPase-Gene pilB1 und pilB2 in adhärenten Zellen im Vergleich zu planktonischen Zellen. Deletion des Archaellen ATPase-Gens flaI führte zu Zellen ohne die 10 nm Filamente, welche nicht mehr motil waren, jedoch weiterhin die 7-8 nm Filamente sowie eine starke Adhäsion aufwiesen. Eine zusätzliche Deletion des Gens pilB1 in einer ΔflaI/ΔpilB1 Doppelmutante reduzierte die Adhäsionsstärke der Zellen drastisch auf 20% des Wildtyps. Demgegenüber ergab eine zusätzliche Deletion des Gens pilB2 keinen weiteren Effekt auf die Adhäsion. Eine bioinformatische Suche nach Genen, welche die Filamentuntereinheiten, d.h. die Piline, codieren, ergab über 30 Kandidaten. Transkriptionelle Untersuchungen mehrerer Kandidaten von besonderem Interesse ergab eine gesteigerte Transkription der mutmaßlichen Pilin-Gene pilA5, pilA6 und pilA7 in adhärenten Zellen, welche verglichen mit dem planktonischen Zustand 2,5- bis 7,1-fach erhöht war. Es wurde eine Proteomanalyse der Biofilmbildung durchgeführt, wobei planktonische sowie frühe und späte Biofilmzellen von Hbt. salinarum R1 untersucht wurden. Eine molekulare Differenzierung der Proteinmuster in Biofilmzellen wurde mittels SDS-PAGE bereits nach einem Tag Biofilmwachstum nachgewiesen. Mittels einer markierungsfreien massenspektrometrischen SWATH-LC/MS/MS Analyse wurde eine hohe Abdeckung des theoretischen Proteoms erzielt, wobei 1629 verschiedene Proteine identifiziert und davon 1464 Proteine quantifiziert wurden, entsprechend 63,2% bzw. 56,8% des Proteoms. In einer relativen Quantifizierung wiesen zwischen 55 und 245 Proteinen starke Veränderungen (> 2-fach) beim Vergleich zweier zellulärer Zustände auf. Es zeigten 882 Proteine statistisch signifikante Veränderungen ihrer Abundanz, entsprechend 60,8% der quantifizierten Proteine bzw. 34,2% des Proteoms. Die deutlichsten Effekte wurden hierbei für Protein involviert in den Energiemetabolismus sowie Proteine des Nukleotid-, Aminosäure- und Lipidmetabolismus beobachtet. Zudem waren Proteine der Proteinbiosynthese sowie zelluläre Prozesse wie Motilität und Signaltransduktion deutlich betroffen. Die Proteomdaten ausgewählter Proteine wurden durch ergänzende transkriptionelle qRT-PCR Analysen validiert. Die vorliegende Arbeit stellt die erste umfassende Beschreibung der Bildung haloarchaeeller Biofilme, am Beispiel von Hbt. salinarum R1, dar.

Deutsch
URN: urn:nbn:de:tuda-tuprints-55835
Sachgruppe der Dewey Dezimalklassifikatin (DDC): 500 Naturwissenschaften und Mathematik > 570 Biowissenschaften, Biologie
Fachbereich(e)/-gebiet(e): 10 Fachbereich Biologie > Microbiology and Archaea
10 Fachbereich Biologie
Hinterlegungsdatum: 24 Jul 2016 19:55
Letzte Änderung: 24 Jul 2016 19:55
PPN:
Referenten: Pfeifer, Prof. Dr. Felicitas ; Kletzin, PD Dr. Arnulf
Datum der mündlichen Prüfung / Verteidigung / mdl. Prüfung: 11 Juli 2016
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