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Mobile Genetic Elements in Methanobacterium Thermoformicicum Mobile genetic elements in Methanobacterium thermoformicicum CENTRALE LANDBOUWCATALOGUS 0000 0426 6769 u BIBLIOTHEEK! fSDSPBOUWUNIVERSHEDi BeAGENINGEM Promotor: Dr. W. M. deVo s hoogleraar in de Bacteriele Genetica Co-promotor: Dr. H. I. L. Eggen universitair docent bij de vakgroep Microbiologic J. Nolling Mobile genetic elements inMethanobacterium thermoformicicum Proefschrift ter verkrijging van de graad van doctor in de landbouw- en milieuwetenschappen op gezag van de rector magnificus, Dr. H. C. van der Plas, in het openbaar te verdedigen op maandag 29 maart 1992 des namiddags te vier uur in de aula van de Landbouwuniversiteit teWageninge n r la b Ko j 99 ' Graag wil ik al diegenen die mij op welke wijze dan ook hebben geholpen bij het tot stand komen van dit proefschrift van harte bedanken. This study was carried out at the Department of Microbiology, Bacterial Genetics Group, Wageningen Agricultural University, The Netherlands. Part of the cover-illustration was taken from an advertisement of the computer company boeder published in:Der Spiegel, 34/1992,p . 118. /..*)ol\;vv , »^"; Stellingen 1. Gezien het grote aantal niet-gekarakteriseerde prokaryoten lijkt de indeling in Archaea en Bacteria door C. R. Woese en medewerkers van voorlopige aard. Woese et al. 1990. Proc. Natl. Acad. Sci. USA287:4576-457 9 2. Het niet in aanmerking nemen van DNA-modifikaties kan bij het in kaart brengen van prokaryotische genomen het trekken van verkeerde conclusies bevorderen. R. Stettler en T. Leisinger (1992). J. Bacterid. 174:7227-7234. 3. De isolatie van thermofiele methanogenen uit riviersedimenten impliceert dat deze organismen wellicht beter als 'fakultatieve thermofielen' beschreven kunnen worden. Dit proefschrift, Hoofdstuk 2 4. Onverwachte resultaten zijn de meest interessante. 5. Vooroordelen tegenover vluchtelingen berusten op vluchtige indrukken. Amnesty International 6. Het aanwakkeren van een oorlogsstemming door nederlandse media tijdens bepaalde internationale voetbalwedstrijden is onaanvaardbaar. 7. Het valt moeilijk te verklaren dat experimentjes met plasmiedjes en faagjes soms leuker kunnen zijn dan rustigjes met een krantje en een pilsje in het zonnetje te zitten. 8. Verkorting van de studieduur bevordert niet de noodzakelijke 'cultuuroverdracht' (de Volkskrant, 09.01.93) aan de universiteit maar versterkt de trend tot opleiding van vakspecialisten met geisoleerde kennis. 9. De aanpak van milieuproblemen wordt belemmerd omdat met onaangename waarheden geen verkiezingen te winnen zijn. 10. Het is aan te bevelen om met het formuleren van stellingen op tijd te beginnen. Stellingen behorende bij het proefschrift "Mobile genetic elements in Methanobacterium thermo- formicicum" van Jork Nolling. Wageningen, 29 maart 1993. AJ/UO82OI, /ka'J Stellingen 1. Gezien het grote aantal niet-gekarakteriseerde prokaryoten lijkt de indeling in Archaea en Bacteria door C. R. Woese en medewerkers van voorlopige aard. Woese et al. 1990. Proc. Natl Acad. ScL VSA 287:4576-4579 2. Het niet in aanmerking nemen van DNA-modifikaties kan bij het in kaart brengen van prokaryotische genomen het trekken van verkeerde conclusies bevorderen. R. Stealer en T. Leisinger (1992). J. Bacterid 174:7227-7234. 3. De isolatie van thermofiele methanogenen uit riviersedimenten impliceert dat deze organismen wellicht beter als 'fakultatieve thermofielen' beschreven kunnen worden. Ditproefschrift , Hoofdstuk 2 4. Onverwachte resultaten zijn de meest interessante. 5. Vooroordelen tegenover vluchtelingen berusten op vluchtigeindnikken . Amnesty International 6. Het aanwakkeren van een oorlogsstemming door nederlandse media tijdens bepaalde Internationale voetbalwedstrijden is onaanvaardbaar. 7. Het valt moeilijk te verklaren dat experimentjes met plasmiedjes en faagjes soms leuker kunnen zijn dan rustigjes met een krantje en een pilsje in het zonnetje te zitten. 8. Verkorting van de studieduur bevordert niet de noodzakelijke 'cultuuroverdracht' {de Volkskrant, 09.01.93) aan de universiteit maar versterkt de trend tot opleiding van vakspecialisten met geisoleerde kennis. 9. De aanpak van milieuproblemen wordt belemmerd omdat met onaangename waarheden geen verkiezingen te winnen zijn. 10. Het is aan te bevelen om met het formuleren van stellingen op tijd te beginnen. Stellingen behorende bij het proefschrift "Mobile genetic elements in Methanobacterium ihermo- formicicmn" van Jork Nolling. Wageningen, 29 maait 1993. Contents Chapter Page 1 GENERAL INTRODUCTION 1 2 Phylogenetic analysis of Methanobacterium sp.: evidence for a 25 formate-utilizing ancestor 3 $F1 and $F3, two novel virulent, archaeal phages infecting different 37 thermophilic strains of the genus Methanobacterium 4 Isolation and characterization of plasmids from different strains 49 of Methanobacterium thermoformicicum 5 Modular organization of related archaeal plasmids encoding 57 different restriction-modification systems in Methanobacterium thermoformicicum 6 Distribution and characterization of plasmid-related sequences 65 in the chromosomal DNA of different thermophilic Methanobacterium strains 7 Characterization of the archaeal, plasmid-encoded type II 83 restriction-modification system MthTl from Methanobacterium thermoformicicum THF: homology to the bacterial NgoPU system from Neisseria gonorrhoeae 8 Identification of the CTAG-recognizing restriction-modification 93 systems MthZl and MthVlfro m Methanobacterium thermoformicicum and characterization of the plasmid-encoded mthZIM gene 9 SUMMARY AND CONCLUDING REMARKS 101 SAMENVATTING 109 APPENDIX A Nucleotide sequence of plasmid pFVI 111 APPENDIX B Nucleotide sequence of plasmid pFZl 117 APPENDIX C Nucleotide sequence of cFR-II 121 CURRICULUM VITAE 122 PUBLICATION LIST 122 CIP-DATA KONINKLIJKE BIBLIOTHEEK, DEN HAAG Nolling, Jork Mobile genetic elements in Methanobacterium thermoformicicum I Jork Nolling. - [S.l. : s.n.]. -111 . Thesis Wageningen. - With ref. - With summary in Dutch. ISBN 90-5485-075-2 Subject headings: molecular genetics /Methanobacterium thermoformicicum. CHAPTER 1 General introduction The diversity of life as the result of evolution from a common origin has generated considerable interest in the classification of organisms. The accuracy, however, with which a phylogenetic tree reflects the relationships among the organisms strongly depends on the markers and methods used for comparison. In general, markers that are directly related to the nucleotide sequences of a genome are more informative for the determination of phylogenetic relationships than are phenotypic properties (157). A nevertheless meaningful phenotypic classification was the division of the living world into the major groups of prokaryotes and eukaryotes which initially was based on readily detectable phenotypic properties such as the pronounced differences in their cellular organization. Only later this distinction was confirmed by the identification of comparable molecular characteristics such as differences in ribosome structure (159). However, the prokaryote-eukaryote dichotomy was based on the comparison of eukaryotic markers with those derived from the model bacterium Escherichia colitha t was considered as a typical representative of the prokaryotic kingdom (159). Compared toth ephenotypi c diversity of eukaryotes, theprokaryote s constitutea grou po f phenotypically relatively homogeneous organisms. This led to the assumption that the prokaryotes have a monophyletic origin, i.e. are descendants of a single common ancestor. Despite thelac k of complex phenotypic markers, prokaryotic systematics was mainly based on comparative morphology of cellso rcolonies , differences in cell-walls revealed by Gram- staining and readily detectable physiological properties such as growth with or without oxygen, nitrogen fixation or photosynthesis (157). However, thosecriteri a haveonl y limited value for prokaryotic taxonomy mainly for two reasons (157). Firstly, lateral gene transfer oradaptatio n toenvironmenta l stress mayhav eresulte d insimila rphenotype so f twodistantl y related organisms. And secondly, the evaluation of aphenotypi c marker as phylogenetically significant is often a subjective one (157). More reliable information on the prokaryotic phylogeny was obtained from analysis of variousmolecula r markers. Cellwal lanalysi san dimmunologica lstudies ,togethe rwit hinitia l approaches ingenotype-base d classification sucha scompariso n of theDN Abas eratio s(GC - content) and analysis of the total DNA relatedness, were applied in the phylogenetic characterization of lower taxa (157). A considerable step forward was the use of macromolecules as 'evolutionary clocks' to determine evolutionary distances (72). Macromolecules such as nucleic acids and proteins consist of alarg e number of independent constituents, i.e. nucleotides and amino acids, whose sequential order provides the information for their function. Sinceth enumbe ro f possibledifferen t sequences isextremel y high, twosequence swit hextensiv esimilarit y aremos tlikel yevolutionar y related rather than the product of convergent evolution. As the result of continuously occurring, selectively neutral mutations, the observed accumulated differences between two sequences are analogous to a relative time span, i.e. the sequence differences can be used to calculate the evolutionary distance of the compared sequences from a common ancestor. Among the sequences that may be used as molecular chronometers for phylogenetic analysis of higher taxa, most suitable ones are those that have been established
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