Molecular Evolution

William F. Martin

 

Member: European Molecular Biology Organization

Member: Northrhine-Westfalian Academy of Science

Fellow: American Academy for Microbiology

  • Endosymbiosis
  • Energy metabolism
  • Eukaryotic anaerobes
  • Evolutionary genome analysis
  • Early evolution

Courses taught:

V419 Introduction to genome analysis

V433 Perl for Biologists

V427 Methods in cell fractionation and proteome analysis

M4406 Biochemistry and evolution of organelles

M4423 Evolution and cell biology of protists

M4449 Advanced genome analysis

Bioinformatics seminar

Literature seminar: Current methods and insights in cell biology

 

Who I am...

I am an evolutionary biologist with an active interest in biochemistry.

My interest in evolution was sparked in 1978 by Willard A. Taber, my undergraduate microbiology teacher at Texas A&M, who during one lecture said "Some people think that chloroplasts arose from free-living cyanobacteria." I wanted to know more. When I finally got around to my first encounter with laboratory research, I jumped at the chance to work with Rüdiger Cerff at the University of Hannover (Germany) on cDNA cloning and sequencing of chloroplast-cytosol isoenzymes for glyceraldehyde-3-phosphate dehydrogenase, GAPDH. The sequences for these isoenzymes offered a test of one of the crucial predictions of endosymbiotic theory, namely that the sequences of nuclear genes for enzymes essential to chloroplast physiology should be more similar to prokaryotic homologues than to the nuclear genes for their cytosolic homologues, which should represent the history of the host that acquired the plastid. If so, that would be evidence for gene transfer to the nucleus in the wake of endosymbiotic origin of plastids (Martin and Cerff, 1986), or endosymbiotic gene transfer, as we later called it (Martin et al., 1993).

My introduction to evolution thus struck roots in a world where most of the genes that plastids have brought into the eukaryotic lineage were expected to be located in the nucleus. My science thus started out in a field where both endosymbiosis and gene transfer in evolution were essential parts of the equation, for how else could one explain why chloroplasts and mitochondria were so similar to modern prokaryotes while harboring only enough organelle DNA to encode for a handful of proteins at best. With an interest in endosymbiosis, and an experimental handle on the topic — molecular evolution — I became very interested in the origin of mitochondria and the nature of the host that acquired the mitochondrion. The host was somehow related to archaea. This led to questions like what kind of archaeon that host might have been, exactly, or what the nature of its physiological interaction with the ancestral mitochondrion at the onset of that symbiosis was. I wanted to know more, but the literature only offered so much in the way of ideas to test.

When one starts probing phases of evolution that go that far back in geological time, issues surrounding the origin of the very first cells is not far off, and since eukaryotes descend from prokaryotes via symbiosis, the origin of life boils down to the origin of prokaryotes, of which there are two very different kinds: bacteria and archaea. One day in 1998, Mike Russell, a geochemist, sent me one of his papers on origin of life and it wasn't too long before we got together and started writing papers together. Mike and I delivered our first paper at a wonderful Royal Society Discussion meeting organized by John F. Allen. At that meeting, I had my first encounter with Nick Lane  — we ended up having a lot of interests in common, and have had a great time writing papers together since.

 

Curriculum vitae

 

How I got here...

I completed my undergraduate degree in Biology at the University of Hannover, completed my PhD in Genetics under the wise and generous supervision of Heinz Saedler at the Max Plank Institute for Breeding Research in Cologne. After my PhD, I returned to Rüdiger Cerff's group, which had moved to the University of Braunschweig, where I worked for 10 happy and productive years. In 1999 I was lucky enough to receive offers for professorships from several German universities, Annette (my wife) decided that I should accept the offer from Düsseldorf, where we have been since.

I have served as an Editor for many journals over the years and I am currently the Editor in Chief of Genome Biology and Evolution.

 

What I do...

My group here in the Institute for Molecular Evolution                                                                  pursues research on the biochemistry and evolution of chloroplasts, mitochondria (including their anaerobic forms, hydrogenosomes), and eukaryotes. We use laboratory experiments and bioinformatic techniques to pursue these questions and to probe even earlier phases of evolution, going back to life's origin, with the help of gene and genome comparisons.

I have published 250 papers, a complete list can be found here, my citation metrics can be found here.

 

Some recent publications.

Weiss MC, Sousa FL, Mrnjavac N, Neukirchen S, Roettger M, Nelson-Sathi S, Martin WF: The physiology and habitat of the last universal common ancestor. Nat Microbiol (2016) in press. doi: 10.1038/NMICROBIOL.2016.116

Ku C, Nelson-Sathi S, Roettger M, Sousa FL, Lockhart PJ, Bryant D, Hazkani-Covo E, McInerney JO, Landan G, Martin WF: Endosymbiotic origin and differential loss of eukaryotic genes. Nature 524:427–432 (2015). PDF

Nelson-Sathi S, Sousa FL, Röttger M, Lozada-Chávez N, Thiergart T, Janssen A, Bryant D, Landan G, Schönheit P, Siebers B, McInerney J, Martin WF: Origins of major archaeal clades correspond to gene acquisitions from bacteria. Nature 517:7780 (2015). PDF

Martin WF, Sousa FL, Lane N: Energy at life's origin. Science 344:1092–1093 (2014). PDF

Sousa F, Martin WF: Biochemical fossils of the ancient transition from geoenergetics to bioenergetics in prokaryotic one carbon compound metabolism. Biochim. Biophys. Acta. 1837:964–981 (2014). PDF

Schmitt V, Menzel D, Händeler K, Gunkel S, Escande ML, Martin WF, Wägele H: Chloroplast incorporation and long-term photosynthetic performance through the life cycle in laboratory cultures of Elysia timida (Sacoglossa, Heterobranchia). Frontiers Zool. 11:15 (2014). PDF

List J-M, Nelson-Sathi S, Geissler H, Martin WF: Networks of lexical borrowing and lateral gene transfer in language and genome evolution. BioEssays 36:141–150 (2014). PDF

Christa G, Zimorski V, Woehle C, Tielens AGM, Wägele H, Martin WF, Gould SB: Plastid-bearing sea slugs fix CO2 in the light but do not require photosynthesis to survive. Proc. Roy. Soc. Lond. B. 281:20132493 (2014). PDF

Zimorski V, Martin WF: Subcellular targeting of proteins and pathways during evolution. New Phytol. 201:1–2 (2014). PDF

de Vries J, Habicht J, Woehle C, Huang C, Christa G, Wägele H, Nickelsen J, Martin WF, Gould SB: Is ftsH the key to plastid longevity in sacoglossan slugs? Genome Biol. Evol. 5:2540–2548 (2013). PDF

Maier U-G, Zauner S, Woehle C, Bolte K, Hempel F, Allen JF, Martin WF: Massively convergent evolution for ribosomal protein gene content in plastid and mitochondrial genomes. Genome Biol. Evol. 5:2318–2329 (2013). PDF  

Zimorski V, Major P, Hoffmann K, Pereira-Brás X, Martin WF, Gould SB: The N-terminal sequences of four major hydrogenosomal proteins are not essential for import into hydrogenosomes of Trichomonas vaginalis. J. Eukaryot. Microbiol.  60:89–97 (2013). PDF

Sousa FL, Shavit-Greivink L, Allen JF, Martin WF: Chlorophyll biosynthesis gene evolution indicates photosystem gene duplication, not photosystem merger, at the origin of oxygenic photosynthesis. Genome Biol. Evol. 5:200–216 (2013). PDF 

Dagan T, Roettger M, Stucken K, Landan G, Koch R, Major P, Gould SB, Goremykin VV, Rippka R, Tandeau de Marsac N, Gugger M, Lockhart PJ, Allen JF, Brune I, Maus I, Pühler A, Martin WF: Section V cyanobacterial genomes and the evolution of oxygenic photosynthesis from prokaryotes to plastids. Genome Biol. Evol. 5:31–44 (2013). PDF

Martin WF: Hydrogen, metals, bifurcating electrons, and proton gradients: The early evolution of biological energy conservation. FEBS Lett. 586:485–493 (2012). PDF

Lane N, Martin WF: The origin of membrane bioenergetics. Cell 151:1406–1416 (2012). PDF

Nelson-Sathi S, Dagan T, Landan G, Janssen A, Steel M, McInerney JO, Deppenmeier U, Martin WF: Acquisition of a thousand eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea. Proc. Natl. Acad. Sci. USA 109:20537–20542 (2012). PDF

Müller M, Mentel M, van Hellemond J, Henze K, Woehle C, Gould SB, Yu R-Y, van der Giezen M, Tielens AGM, Martin WF: Biochemistry and evolution of anaerobic energy metabolism in eukaryotes. Microbiol. Mol. Biol. Rev. 76:444–495 (2012). PDF

McInerney JO, Martin WF, Koonin EV, Allen JF, Galperin MY, Lane N, Archibald JM, Embley TM: Planctomycetes and eukaryotes: a case of analogy not homology. BioEssays 33:810–817 (2011). PDF

Wägele H, Deusch O, Händeler K, Martin R, Schmitt V, Christa G, Pinzger B, Dagan T,  Klussmann-Kolb A, Martin W: Transcriptomic evidence that longevity of acquired plastids in the photosynthetic slugs Elysia timida and Plakobranchus ocellatus does not entail lateral transfer of algal nuclear genes. Mol. Biol. Evol. 28:699–706 (2011). PDF

Lane N, Martin W: The energetics of genome complexity. Nature 467:929–934 (2010). PDF

Dagan T, Roettger M, Bryant D, Martin W: Genome networks root the tree of life between prokaryotic domains. Genome Biol. Evol. 2:379–392 (2010). PDF

Russell MJ, Hall AJ, Martin W: Serpentinization as a source of energy at the origin of life. Geobiology. 8:355–371 (2010). pubmed

Mentel M, Martin W: Anaerobic animals from an ancient, anoxic ecological niche. BMC Biology. 8:32 [6 pages] (2010). PDF

Lane N, Allen JF, Martin W: How did LUCA make a living? Chemiosmosis in the origin of life. BioEssays 32:271–280 (2010). PDF

Hazkani-Covo E, Zeller RM, Martin W: Molecular poltergeists: mitochondrial DNA copies (numts) in sequenced nuclear genomes. PLoS Genet. 6:e1000834 (2010). PDF

Dagan T, Martin W: Seeing red and green in diatom genomes. Science 324:1651–1652 (2009). PDF

Martin W: Hydrothermalquellen und der Ursprung des Lebens. Biologie in Unserer Zeit 39:166–174 (2009). PDF

Martin W, Baross J, Kelley D, Russell MJ: Hydrothermal vents and the origin of life. Nature Rev. Microbiol. 6:805–814 (2008). PDF

Dagan T, Artzy-Randrup Y, Martin W: Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proc. Natl. Acad. Sci. USA 105:10039–10044 (2008). PDF

Allen JF, Martin W: Evolutionary biology: Out of thin air. Nature 445:610–612 (2007). PDF

Dagan T, Martin W: Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution. Proc. Natl. Acad. Sci. USA 104:870–875 (2007). PDF

Martin W, Russell MJ: On the origin of biochemistry at an alkaline hydrothermal vent. Phil. Trans Roy. Soc. Lond. B 362:1887–1925 (2007). PDF

Dagan T, Martin W: The tree of one percent. Genome Biol. 7:118 [7 pages] (2006). PDF

Embley TM, Martin W: Eukaryote evolution: changes and challenges. Nature 440:623–630 (2006). PDF

Martin W, Koonin EV: Introns and the origin of nucleus-cytosol compartmentation. Nature 440:41–45 (2006). PDF

Institutsleitung

Prof. Dr. William F. Martin

Molekulare Evolution
Heinrich-Heine-Universität
Düsseldorf
Universitätsstraße 1
Gebäude: 26.13
Etage/Raum: 01.34
Tel.: +49 211 81-13011
Fax: +49 211 81-13554
Verantwortlich für den Inhalt: E-Mail sendenProf. Dr. William F. Martin