William Martin | University of Düsseldorf (original) (raw)
Papers by William Martin
Cold Spring Harbor perspectives in biology, Jan 18, 2015
In this article, the term "early microbial evolution" refers to the phase of biological... more In this article, the term "early microbial evolution" refers to the phase of biological history from the emergence of life to the diversification of the first microbial lineages. In the modern era (since we knew about archaea), three debates have emerged on the subject that deserve discussion: (1) thermophilic origins versus mesophilic origins, (2) autotrophic origins versus heterotrophic origins, and (3) how do eukaryotes figure into early evolution. Here, we revisit those debates from the standpoint of newer data. We also consider the perhaps more pressing issue that molecular phylogenies need to recover anaerobic lineages at the base of prokaryotic trees, because O2 is a product of biological evolution; hence, the first microbes had to be anaerobes. If molecular phylogenies do not recover anaerobes basal, something is wrong. Among the anaerobes, hydrogen-dependent autotrophs-acetogens and methanogens-look like good candidates for the ancestral state of physiology in the...
Nature microbiology, Jan 25, 2016
The concept of a last universal common ancestor of all cells (LUCA, or the progenote) is central ... more The concept of a last universal common ancestor of all cells (LUCA, or the progenote) is central to the study of early evolution and life's origin, yet information about how and where LUCA lived is lacking. We investigated all clusters and phylogenetic trees for 6.1 million protein coding genes from sequenced prokaryotic genomes in order to reconstruct the microbial ecology of LUCA. Among 286,514 protein clusters, we identified 355 protein families (∼0.1%) that trace to LUCA by phylogenetic criteria. Because these proteins are not universally distributed, they can shed light on LUCA's physiology. Their functions, properties and prosthetic groups depict LUCA as anaerobic, CO2-fixing, H2-dependent with a Wood-Ljungdahl pathway, N2-fixing and thermophilic. LUCA's biochemistry was replete with FeS clusters and radical reaction mechanisms. Its cofactors reveal dependence upon transition metals, flavins, S-adenosyl methionine, coenzyme A, ferredoxin, molybdopterin, corrins and...
Like programs written in general-purpose languages, programs written in DSLs may also suffer from... more Like programs written in general-purpose languages, programs written in DSLs may also suffer from tangling and scattering in the presence of domain-specific crosscutting concerns. This paper presents an architecture that supports aspect-oriented features for domain-specific base languages. Both base programs and advices are written in different domain-specific languages. The framework relies on the concept of domain-specific join point.
Physics Letters B, 2013
Results are presented from a search for a W boson using a dataset corresponding to 5.0 fb −1 of i... more Results are presented from a search for a W boson using a dataset corresponding to 5.0 fb −1 of integrated luminosity collected during 2011 by the CMS experiment at the LHC in pp collisions at √ s = 7 TeV. The W boson is modeled as a heavy W boson, but different scenarios for the couplings to fermions are considered, involving both lefthanded and right-handed chiral projections of the fermions, as well as an arbitrary mixture of the two. The search is performed in the decay channel W → tb, leading to a final state signature with a single electron or muon, missing transverse energy, and jets, at least one of which is identified as a b-jet. A W boson that couples to the right-handed (left-handed) chiral projections of the fermions with the same coupling constants as the W is excluded for masses below 1.85 (1.51) TeV at the 95% confidence level. For the first time using LHC data, constraints on the W gauge couplings for a set of left-and right-handed coupling combinations have been placed. These results represent a significant improvement over previously published limits.
Nature, 2015
The mechanisms that underlie the origin of major prokaryotic groups are poorly understood. In pri... more The mechanisms that underlie the origin of major prokaryotic groups are poorly understood. In principle, the origin of both species and higher taxa among prokaryotes should entail similar mechanisms--ecological interactions with the environment paired with natural genetic variation involving lineage-specific gene innovations and lineage-specific gene acquisitions. To investigate the origin of higher taxa in archaea, we have determined gene distributions and gene phylogenies for the 267,568 protein-coding genes of 134 sequenced archaeal genomes in the context of their homologues from 1,847 reference bacterial genomes. Archaeal-specific gene families define 13 traditionally recognized archaeal higher taxa in our sample. Here we report that the origins of these 13 groups unexpectedly correspond to 2,264 group-specific gene acquisitions from bacteria. Interdomain gene transfer is highly asymmetric, transfers from bacteria to archaea are more than fivefold more frequent than vice versa. ...
Vaccine, 2009
Francisella tularensis, the etiological agent of tularemia, is one of the most infectious bacteri... more Francisella tularensis, the etiological agent of tularemia, is one of the most infectious bacterial pathogens known. No vaccine is currently approved for public use. Previously, we identified epitopes recognized specifically by T cells obtained from individuals following infection with F. tularensis. Here, we report that a subunit vaccine constructed based upon these epitopes elicited protective immunity in "humanized" HLA class II (DRB1*0401) transgenic mice. Vaccinated mice challenged intratracheally with a lethal dose of F. tularensis (Live Vaccine Strain) exhibited a rapid increase in pro-inflammatory cytokine production and diminished number of organisms in the lungs, and a concurrent increased rate of survival. These results demonstrate the efficacy of an epitope-based tularemia vaccine and suggest that such an approach might be widely applicable to the development of vaccines specific for intracellular bacterial pathogens.
Trends in Genetics, 1999
Genes in mitochondria and chloroplasts are co-located with their gene products to permit regulati... more Genes in mitochondria and chloroplasts are co-located with their gene products to permit regulation of trans-membrane electron transport at the energetic boundary of the cell.
Trends in Biochemical Sciences, 2004
Science, 2007
In their Review “Genomics and the irreducible nature of eukaryote cells” (19 May 2006, p. [1011][... more In their Review “Genomics and the irreducible nature of eukaryote cells” (19 May 2006, p. [1011][1]), C. G. Kurland et al. purport to “review recent data from proteomics and genome sequences,” but delivered only biased opinions. Asserting genome sequence evidence to suggest “that
Science, 2009
A survey of genetic diversity of cattle suggests two domestication events in Asia and selection b... more A survey of genetic diversity of cattle suggests two domestication events in Asia and selection by husbandry.
Protist, 2000
Cryptomonads and chlorarachniophytes acquired photosynthesis independently by engulfing and retai... more Cryptomonads and chlorarachniophytes acquired photosynthesis independently by engulfing and retaining eukaryotic algal cells. The nucleus of the engulfed cells (known as a nucleomorph) is much reduced and encodes only a handful of the numerous essential plastid proteins normally encoded by the nucleus of chloroplast-containing organisms. In cryptomonads and chlorarachniophytes these proteins are thought to be encoded by genes in the secondary host nucleus. Genes for these proteins were potentially transferred from the nucleomorph (symbiont nucleus) to the secondary host nucleus; nucleus to nucleus intracellular gene transfers. We isolated complementary DNA clones (cDNAs) for chlorophyll-binding proteins from a cryptomonad and a chlorarachniophyte. In each organism these genes reside in the secondary host nuclei, but phylogenetic evidence, and analysis of the targeting mechanisms, suggest the genes were initially in the respective nucleomorphs (symbiont nuclei). Implications for origins of secondary endosymbiotic algae are discussed.
PLoS Biology, 2004
The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intrace... more The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are found in a variety of invertebrate species, are of great interest due to their diverse interactions with different hosts, which range from many forms of reproductive parasitism to mutualistic symbioses. Analysis of the wMel genome, in particular phylogenomic comparisons with other intracellular bacteria, has revealed many insights into the biology and evolution of wMel and Wolbachia in general. For example, the wMel genome is unique among sequenced obligate intracellular species in both being highly streamlined and containing very high levels of repetitive DNA and mobile DNA elements. This observation, coupled with multiple evolutionary reconstructions, suggests that natural selection is somewhat inefficient in wMel, most likely owing to the occurrence of repeated population bottlenecks. Genome analysis predicts many metabolic differences with the closely related Rickettsia species, including the presence of intact glycolysis and purine synthesis, which may compensate for an inability to obtain ATP directly from its host, as Rickettsia can. Other discoveries include the apparent inability of wMel to synthesize lipopolysaccharide and the presence of the most genes encoding proteins with ankyrin repeat domains of any prokaryotic genome yet sequenced. Despite the ability of wMel to infect the germline of its host, we find no evidence for either recent lateral gene transfer between wMel and D. melanogaster or older transfers between Wolbachia and any host. Evolutionary analysis further supports the hypothesis that mitochondria share a common ancestor with the a-Proteobacteria, but shows little support for the grouping of mitochondria with species in the order Rickettsiales. With the availability of the complete genomes of both species and excellent genetic tools for the host, the wMel-D. melanogaster symbiosis is now an ideal system for studying the biology and evolution of Wolbachia infections.
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](Physical Review Letters, 2012
Philosophical Transactions of the Royal Society B: Biological Sciences, 2007
A model for the origin of biochemistry at an alkaline hydrothermal vent has been developed that f... more A model for the origin of biochemistry at an alkaline hydrothermal vent has been developed that focuses on the acetyl-CoA (Wood–Ljungdahl) pathway of CO 2 fixation and central intermediary metabolism leading to the synthesis of the constituents of purines and pyrimidines. The idea that acetogenesis and methanogenesis were the ancestral forms of energy metabolism among the first free-living eubacteria and archaebacteria, respectively, stands in the foreground. The synthesis of formyl pterins, which are essential intermediates of the Wood–Ljungdahl pathway and purine biosynthesis, is found to confront early metabolic systems with steep bioenergetic demands that would appear to link some, but not all, steps of CO 2 reduction to geochemical processes in or on the Earth's crust. Inorganically catalysed prebiotic analogues of the core biochemical reactions involved in pterin-dependent methyl synthesis of the modern acetyl-CoA pathway are considered. The following compounds appear as p...
Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, 2003
All life is organized as cells. Physical compartmentation from the environment and self–organizat... more All life is organized as cells. Physical compartmentation from the environment and self–organization of self–contained redox reactions are the most conserved attributes of living things, hence inorganic matter with such attributes would be life's most likely forebear. We propose that life evolved in structured iron monosulphide precipitates in a seepage site hydrothermal mound at a redox, pH and temperature gradient between sulphide–rich hydrothermal fluid and iron(II)–containing waters of the Hadean ocean floor. The naturally arising, three–dimensional compartmentation observed within fossilized seepage–site metal sulphide precipitates indicates that these inorganic compartments were the precursors of cell walls and membranes found in free–living prokaryotes. The known capability of FeS and NiS to catalyse the synthesis of the acetyl–methylsulphide from carbon monoxide and methylsulphide, constituents of hydrothermal fluid, indicates that pre–biotic syntheses occurred at the in...
Nature Reviews Microbiology, 2008
The chemistry of life is the chemistry of reduced organic compounds, and therefore all theories f... more The chemistry of life is the chemistry of reduced organic compounds, and therefore all theories for the origin of life must offer testable hypotheses to account for the source of these compounds. The bestknown theories for the origin of organic compounds are based on the notion of an 'organic soup' that was generated either by lightning-driven reactions in the early atmosphere of the Earth or by delivery of organic compounds to the Earth from space (BOX 1). When submarine hydrothermal vents were discovered 30 years ago, hypotheses on the source of life's reduced carbon started to change. Hydrothermal vents revealed a vast and previously unknown domain of chemistry on the Earth. These vents harbour rich ecosystems, the energy source of which stems mainly from mid-oceanridge volcanism 1,2. The 360°C sulphide chimneys of the vent systems are primordial environments that are reminiscent of early Earth, with reactive gases, dissolved elements, and thermal and chemical gradients that operate over spatial scales of centimetres to metres. This discovery had an immediate impact on hypotheses about the origin of life, because it was recognized that the vent systems were chemically reactive environments that constituted suitable conditions for sustained prebiotic syntheses 3. In 2000, a completely new type of vent system was discovered that is characterized by carbonate chimneys that rise 60 metres above the ultramafic sea-floor 4,5. This vent system was named the Lost City hydrothermal field (LCHF), and might be particularly relevant to our understanding of the origins of life. The ultramafic underpinnings of the Lost City system have a similar chemical composition to lavas that erupted into the primordial oceans on early Earth 5,6. Consequently, the LCHF provides insights into past mantle geochemistry and presents a better understanding of the chemical constraints that existed during the evolutionary transition from geochemical to biochemical processes. Hydrothermal vents occur at sea-floor spreading zones and have a global distribution (FIG. 1): vent systems have been discovered at almost all sea-floor locations that have been studied in detail 7. At spreading zones, magma chambers that contain molten rock (800-1,200°C) discharge lavas onto the ocean floor over time periods that range from <10 years between eruptions to >50,000 years between eruptions 8. These eruptions produce black smokers and associated diffuse flow systems that host dense and diverse biological communities 9,10. By contrast, the mountains of the Lost City-like systems are tens of kilometres off-axis, rarely contain volcanic rocks and are formed by sustained fault activity that has lasted for millions of years 4,5,11. Lost City systems are profoundly different from black smokers, so it is important to contrast the two (for an in-depth comparison of Lost City systems and black smokers, see REF. 12). Black smokers Examples of black smokers, such as the Faulty Towers complex (FIG. 2a), are located directly above magma chambers that are found 1-3 kilometres beneath the seafloor 12. Black smoker chimneys emit hot (up to 405°C), chemically modified seawater 13. Beneath the fissured sea-floor, downwelling seawater comes into close contact with the magma chamber during its circulation from the ocean floor, before moving through the crust to re-emerge at the vents. Effluent at black smokers is typically acidic (pH 2-3) and rich in dissolved transition metals 14 , such as Fe(II) and Mn(II). Because the black smoker systems are fuelled by volcanoes, black smoker fluids commonly contain high concentrations of
Molecular Biology and Evolution, 2006
Eukaryotic gene fusion and fission events are mechanistically more complicated than in prokaryote... more Eukaryotic gene fusion and fission events are mechanistically more complicated than in prokaryotes, and their quantitative contributions to genome evolution are still poorly understood. We have identified all differentially composite or split genes in 2 fully sequenced plant genomes, Oryza sativa and Arabidopsis thaliana. Out of 10,172 orthologous gene pairs, 60 (0.6% of the total) revealed a verified fusion or fission event in either lineage after the divergence of O. sativa and A. thaliana. Polarizing these events by outgroup comparison revealed differences in the rate of gene fission but not of gene fusion in the rice and Arabidopsis lineages. Gene fission occurred at a higher rate than gene fusion in the O. sativa lineage and was furthermore more common in rice than in Arabidopsis. Nucleotide insertion bias has promoted gene fission in the O. sativa lineage, consistent with its generally longer nucleotide sequences than A. thaliana in selectively neutral regions, and with the abundance of transposable elements in rice. The divergence time of monocots and dicots (140-200 Myr) indicates that gene fusion/fission events occur at an average rate of 1 3 10 À11 to 2 3 10 À11 events per gene per year, ;100fold slower than the average per site nuclear nucleotide substitution rate in these lineages. Gene fusion and fission are thus rare and slow processes in higher plant genomes; they should be of utility to address deeper evolutionary relationships among plants-and the relationship of plants to other eukaryotic lineages-where sequence-based phylogenies provide equivocal or conflicting results. Recently, the genome sequence of rice, Oryza sativa (O. sativa L. ssp. japonica cv. Nipponbare), has been determined. Its gene repertoire was quite thoroughly annotated using full-length cDNA libraries (International Rice Genome Sequencing Project 2005; Ohyanagi et al. 2006). This permits a monocot-dicot comparison to the Arabidopsis thaliana genome (Arabidopsis Genome Initiative 2000). Here, we addressed the evolutionary dynamics of gene fusion and fission events in these plant genomes. We identify all of the candidates of gene fusion or fission events, which have occurred after the divergence of O. sativa and A. thaliana. We report the number and rate of the events including all genes and coordinates involved as well as their functional annotations and reconstruct the evolutionary scenario of differential gene fusion and fission in each lineage. Materials and Methods Protein Sequences in O. sativa and A. thaliana We collected a total of 40,041 protein sequences in O. sativa genomes annotated in the Rice Annotation Project (RAP) as of 14 June 2005 (Ohyanagi et al. 2006) and 28,860 protein sequences in A. thaliana in GenBank. We then checked the locations of protein-coding genes on genomes and whether their overlap was due to alternative splicing or redundant annotation, using longer ones if locations overlapped. This yielded a total of 28,759 protein sequences from O. sativa and 26,364 sequences from A. thaliana. Among those O. sativa sequences, 21,818 are supported by full-length cDNA in RAP. To check the A. thaliana sequences, we downloaded 15,295 full-length cDNA records as of 24 May 2005 from RIKEN ftp site (http:// rarge.gsc.riken.jp/archives/rafl/sequence/) and confirmed
Geochimica et Cosmochimica Acta, 1989
Aktnct-Organic carbon oxidation rates in San Clemente Besin wm &term&d by benthic chamber experim... more Aktnct-Organic carbon oxidation rates in San Clemente Besin wm &term&d by benthic chamber experiments using the Bottom Lander, along with studies of pore water chemi&y. Non-steady-state diagenetic models are developed for interp&ng concentration-time data from the benthic chamber experiments. 4, NOi, and a-81~ all important oxidsnts for orgsnic carbon at our study site. Regenerated fixed nitrogen WBS consumed by NO; reduction. Ikerr is a tlux of NO j into the sediments, and the benthic flux of NHt is undetectable. The total rate at which fixed nitrogen is removal from the oceans at this she is about twice the flux of PON to the sea floor. Si@ fluxes calculated from interfacial pore water gradients are in satisfactory agreement with those determined using the Lander. Most sika dissolution must therefore occur within the sediment.% although interstitial profiles show that little dkolution occurs below I cm depth. INTRODUCIION A UNIFIED VIEW of early diageneais in pelagic sediments has developed over the last decade. Sedimentary organic carbon is oxidized Jequentially by 02, NO;, MnOz, Fe203 and SO$-. The order reflects the free energy of C, oxidation, and is manifested by a characteristic pattern of depth variability in pore water concentrations of 02, NO;, Mn2+, Fti+, a-, TA (total alkalinity), TCOZ (total a), and other species (FROEUCH et al., 1979; EMERSON er al., 1980, and otbers). Concentrations of these variables covary in ways &Ming the stoichiometry of the G degradation dons (SHOL
Geobiology, 2010
For life to have emerged from CO 2 , rocks, and water on the early Earth, a sustained source of c... more For life to have emerged from CO 2 , rocks, and water on the early Earth, a sustained source of chemically transducible energy was essential. The serpentinization process is emerging as an increasingly likely source of that energy. Serpentinization of ultramafic crust would have continuously supplied hydrogen, methane, minor formate, and ammonia, as well as calcium and traces of acetate, molybdenum and tungsten, to off-ridge alkaline hydrothermal springs that interfaced with the metal-rich carbonic Hadean Ocean. Silica and bisulfide were also delivered to these springs where cherts and sulfides were intersected by the alkaline solutions. The proton and redox gradients so generated represent a rich source of naturally produced chemiosmotic energy, stemming from geochemistry that merely had to be tapped, rather than induced, by the earliest biochemical systems. Hydrothermal mounds accumulating at similar sites in today's oceans offer conceptual and experimental models for the chemistry germane to the emergence of life, although the ubiquity of microbial communities at such sites in addition to our oxygenated atmosphere preclude an exact analogy.
Cold Spring Harbor perspectives in biology, Jan 18, 2015
In this article, the term "early microbial evolution" refers to the phase of biological... more In this article, the term "early microbial evolution" refers to the phase of biological history from the emergence of life to the diversification of the first microbial lineages. In the modern era (since we knew about archaea), three debates have emerged on the subject that deserve discussion: (1) thermophilic origins versus mesophilic origins, (2) autotrophic origins versus heterotrophic origins, and (3) how do eukaryotes figure into early evolution. Here, we revisit those debates from the standpoint of newer data. We also consider the perhaps more pressing issue that molecular phylogenies need to recover anaerobic lineages at the base of prokaryotic trees, because O2 is a product of biological evolution; hence, the first microbes had to be anaerobes. If molecular phylogenies do not recover anaerobes basal, something is wrong. Among the anaerobes, hydrogen-dependent autotrophs-acetogens and methanogens-look like good candidates for the ancestral state of physiology in the...
Nature microbiology, Jan 25, 2016
The concept of a last universal common ancestor of all cells (LUCA, or the progenote) is central ... more The concept of a last universal common ancestor of all cells (LUCA, or the progenote) is central to the study of early evolution and life's origin, yet information about how and where LUCA lived is lacking. We investigated all clusters and phylogenetic trees for 6.1 million protein coding genes from sequenced prokaryotic genomes in order to reconstruct the microbial ecology of LUCA. Among 286,514 protein clusters, we identified 355 protein families (∼0.1%) that trace to LUCA by phylogenetic criteria. Because these proteins are not universally distributed, they can shed light on LUCA's physiology. Their functions, properties and prosthetic groups depict LUCA as anaerobic, CO2-fixing, H2-dependent with a Wood-Ljungdahl pathway, N2-fixing and thermophilic. LUCA's biochemistry was replete with FeS clusters and radical reaction mechanisms. Its cofactors reveal dependence upon transition metals, flavins, S-adenosyl methionine, coenzyme A, ferredoxin, molybdopterin, corrins and...
Like programs written in general-purpose languages, programs written in DSLs may also suffer from... more Like programs written in general-purpose languages, programs written in DSLs may also suffer from tangling and scattering in the presence of domain-specific crosscutting concerns. This paper presents an architecture that supports aspect-oriented features for domain-specific base languages. Both base programs and advices are written in different domain-specific languages. The framework relies on the concept of domain-specific join point.
Physics Letters B, 2013
Results are presented from a search for a W boson using a dataset corresponding to 5.0 fb −1 of i... more Results are presented from a search for a W boson using a dataset corresponding to 5.0 fb −1 of integrated luminosity collected during 2011 by the CMS experiment at the LHC in pp collisions at √ s = 7 TeV. The W boson is modeled as a heavy W boson, but different scenarios for the couplings to fermions are considered, involving both lefthanded and right-handed chiral projections of the fermions, as well as an arbitrary mixture of the two. The search is performed in the decay channel W → tb, leading to a final state signature with a single electron or muon, missing transverse energy, and jets, at least one of which is identified as a b-jet. A W boson that couples to the right-handed (left-handed) chiral projections of the fermions with the same coupling constants as the W is excluded for masses below 1.85 (1.51) TeV at the 95% confidence level. For the first time using LHC data, constraints on the W gauge couplings for a set of left-and right-handed coupling combinations have been placed. These results represent a significant improvement over previously published limits.
Nature, 2015
The mechanisms that underlie the origin of major prokaryotic groups are poorly understood. In pri... more The mechanisms that underlie the origin of major prokaryotic groups are poorly understood. In principle, the origin of both species and higher taxa among prokaryotes should entail similar mechanisms--ecological interactions with the environment paired with natural genetic variation involving lineage-specific gene innovations and lineage-specific gene acquisitions. To investigate the origin of higher taxa in archaea, we have determined gene distributions and gene phylogenies for the 267,568 protein-coding genes of 134 sequenced archaeal genomes in the context of their homologues from 1,847 reference bacterial genomes. Archaeal-specific gene families define 13 traditionally recognized archaeal higher taxa in our sample. Here we report that the origins of these 13 groups unexpectedly correspond to 2,264 group-specific gene acquisitions from bacteria. Interdomain gene transfer is highly asymmetric, transfers from bacteria to archaea are more than fivefold more frequent than vice versa. ...
Vaccine, 2009
Francisella tularensis, the etiological agent of tularemia, is one of the most infectious bacteri... more Francisella tularensis, the etiological agent of tularemia, is one of the most infectious bacterial pathogens known. No vaccine is currently approved for public use. Previously, we identified epitopes recognized specifically by T cells obtained from individuals following infection with F. tularensis. Here, we report that a subunit vaccine constructed based upon these epitopes elicited protective immunity in "humanized" HLA class II (DRB1*0401) transgenic mice. Vaccinated mice challenged intratracheally with a lethal dose of F. tularensis (Live Vaccine Strain) exhibited a rapid increase in pro-inflammatory cytokine production and diminished number of organisms in the lungs, and a concurrent increased rate of survival. These results demonstrate the efficacy of an epitope-based tularemia vaccine and suggest that such an approach might be widely applicable to the development of vaccines specific for intracellular bacterial pathogens.
Trends in Genetics, 1999
Genes in mitochondria and chloroplasts are co-located with their gene products to permit regulati... more Genes in mitochondria and chloroplasts are co-located with their gene products to permit regulation of trans-membrane electron transport at the energetic boundary of the cell.
Trends in Biochemical Sciences, 2004
Science, 2007
In their Review “Genomics and the irreducible nature of eukaryote cells” (19 May 2006, p. [1011][... more In their Review “Genomics and the irreducible nature of eukaryote cells” (19 May 2006, p. [1011][1]), C. G. Kurland et al. purport to “review recent data from proteomics and genome sequences,” but delivered only biased opinions. Asserting genome sequence evidence to suggest “that
Science, 2009
A survey of genetic diversity of cattle suggests two domestication events in Asia and selection b... more A survey of genetic diversity of cattle suggests two domestication events in Asia and selection by husbandry.
Protist, 2000
Cryptomonads and chlorarachniophytes acquired photosynthesis independently by engulfing and retai... more Cryptomonads and chlorarachniophytes acquired photosynthesis independently by engulfing and retaining eukaryotic algal cells. The nucleus of the engulfed cells (known as a nucleomorph) is much reduced and encodes only a handful of the numerous essential plastid proteins normally encoded by the nucleus of chloroplast-containing organisms. In cryptomonads and chlorarachniophytes these proteins are thought to be encoded by genes in the secondary host nucleus. Genes for these proteins were potentially transferred from the nucleomorph (symbiont nucleus) to the secondary host nucleus; nucleus to nucleus intracellular gene transfers. We isolated complementary DNA clones (cDNAs) for chlorophyll-binding proteins from a cryptomonad and a chlorarachniophyte. In each organism these genes reside in the secondary host nuclei, but phylogenetic evidence, and analysis of the targeting mechanisms, suggest the genes were initially in the respective nucleomorphs (symbiont nuclei). Implications for origins of secondary endosymbiotic algae are discussed.
PLoS Biology, 2004
The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intrace... more The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are found in a variety of invertebrate species, are of great interest due to their diverse interactions with different hosts, which range from many forms of reproductive parasitism to mutualistic symbioses. Analysis of the wMel genome, in particular phylogenomic comparisons with other intracellular bacteria, has revealed many insights into the biology and evolution of wMel and Wolbachia in general. For example, the wMel genome is unique among sequenced obligate intracellular species in both being highly streamlined and containing very high levels of repetitive DNA and mobile DNA elements. This observation, coupled with multiple evolutionary reconstructions, suggests that natural selection is somewhat inefficient in wMel, most likely owing to the occurrence of repeated population bottlenecks. Genome analysis predicts many metabolic differences with the closely related Rickettsia species, including the presence of intact glycolysis and purine synthesis, which may compensate for an inability to obtain ATP directly from its host, as Rickettsia can. Other discoveries include the apparent inability of wMel to synthesize lipopolysaccharide and the presence of the most genes encoding proteins with ankyrin repeat domains of any prokaryotic genome yet sequenced. Despite the ability of wMel to infect the germline of its host, we find no evidence for either recent lateral gene transfer between wMel and D. melanogaster or older transfers between Wolbachia and any host. Evolutionary analysis further supports the hypothesis that mitochondria share a common ancestor with the a-Proteobacteria, but shows little support for the grouping of mitochondria with species in the order Rickettsiales. With the availability of the complete genomes of both species and excellent genetic tools for the host, the wMel-D. melanogaster symbiosis is now an ideal system for studying the biology and evolution of Wolbachia infections.
Physical Review Letters, 2012
Philosophical Transactions of the Royal Society B: Biological Sciences, 2007
A model for the origin of biochemistry at an alkaline hydrothermal vent has been developed that f... more A model for the origin of biochemistry at an alkaline hydrothermal vent has been developed that focuses on the acetyl-CoA (Wood–Ljungdahl) pathway of CO 2 fixation and central intermediary metabolism leading to the synthesis of the constituents of purines and pyrimidines. The idea that acetogenesis and methanogenesis were the ancestral forms of energy metabolism among the first free-living eubacteria and archaebacteria, respectively, stands in the foreground. The synthesis of formyl pterins, which are essential intermediates of the Wood–Ljungdahl pathway and purine biosynthesis, is found to confront early metabolic systems with steep bioenergetic demands that would appear to link some, but not all, steps of CO 2 reduction to geochemical processes in or on the Earth's crust. Inorganically catalysed prebiotic analogues of the core biochemical reactions involved in pterin-dependent methyl synthesis of the modern acetyl-CoA pathway are considered. The following compounds appear as p...
Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, 2003
All life is organized as cells. Physical compartmentation from the environment and self–organizat... more All life is organized as cells. Physical compartmentation from the environment and self–organization of self–contained redox reactions are the most conserved attributes of living things, hence inorganic matter with such attributes would be life's most likely forebear. We propose that life evolved in structured iron monosulphide precipitates in a seepage site hydrothermal mound at a redox, pH and temperature gradient between sulphide–rich hydrothermal fluid and iron(II)–containing waters of the Hadean ocean floor. The naturally arising, three–dimensional compartmentation observed within fossilized seepage–site metal sulphide precipitates indicates that these inorganic compartments were the precursors of cell walls and membranes found in free–living prokaryotes. The known capability of FeS and NiS to catalyse the synthesis of the acetyl–methylsulphide from carbon monoxide and methylsulphide, constituents of hydrothermal fluid, indicates that pre–biotic syntheses occurred at the in...
Nature Reviews Microbiology, 2008
The chemistry of life is the chemistry of reduced organic compounds, and therefore all theories f... more The chemistry of life is the chemistry of reduced organic compounds, and therefore all theories for the origin of life must offer testable hypotheses to account for the source of these compounds. The bestknown theories for the origin of organic compounds are based on the notion of an 'organic soup' that was generated either by lightning-driven reactions in the early atmosphere of the Earth or by delivery of organic compounds to the Earth from space (BOX 1). When submarine hydrothermal vents were discovered 30 years ago, hypotheses on the source of life's reduced carbon started to change. Hydrothermal vents revealed a vast and previously unknown domain of chemistry on the Earth. These vents harbour rich ecosystems, the energy source of which stems mainly from mid-oceanridge volcanism 1,2. The 360°C sulphide chimneys of the vent systems are primordial environments that are reminiscent of early Earth, with reactive gases, dissolved elements, and thermal and chemical gradients that operate over spatial scales of centimetres to metres. This discovery had an immediate impact on hypotheses about the origin of life, because it was recognized that the vent systems were chemically reactive environments that constituted suitable conditions for sustained prebiotic syntheses 3. In 2000, a completely new type of vent system was discovered that is characterized by carbonate chimneys that rise 60 metres above the ultramafic sea-floor 4,5. This vent system was named the Lost City hydrothermal field (LCHF), and might be particularly relevant to our understanding of the origins of life. The ultramafic underpinnings of the Lost City system have a similar chemical composition to lavas that erupted into the primordial oceans on early Earth 5,6. Consequently, the LCHF provides insights into past mantle geochemistry and presents a better understanding of the chemical constraints that existed during the evolutionary transition from geochemical to biochemical processes. Hydrothermal vents occur at sea-floor spreading zones and have a global distribution (FIG. 1): vent systems have been discovered at almost all sea-floor locations that have been studied in detail 7. At spreading zones, magma chambers that contain molten rock (800-1,200°C) discharge lavas onto the ocean floor over time periods that range from <10 years between eruptions to >50,000 years between eruptions 8. These eruptions produce black smokers and associated diffuse flow systems that host dense and diverse biological communities 9,10. By contrast, the mountains of the Lost City-like systems are tens of kilometres off-axis, rarely contain volcanic rocks and are formed by sustained fault activity that has lasted for millions of years 4,5,11. Lost City systems are profoundly different from black smokers, so it is important to contrast the two (for an in-depth comparison of Lost City systems and black smokers, see REF. 12). Black smokers Examples of black smokers, such as the Faulty Towers complex (FIG. 2a), are located directly above magma chambers that are found 1-3 kilometres beneath the seafloor 12. Black smoker chimneys emit hot (up to 405°C), chemically modified seawater 13. Beneath the fissured sea-floor, downwelling seawater comes into close contact with the magma chamber during its circulation from the ocean floor, before moving through the crust to re-emerge at the vents. Effluent at black smokers is typically acidic (pH 2-3) and rich in dissolved transition metals 14 , such as Fe(II) and Mn(II). Because the black smoker systems are fuelled by volcanoes, black smoker fluids commonly contain high concentrations of
Molecular Biology and Evolution, 2006
Eukaryotic gene fusion and fission events are mechanistically more complicated than in prokaryote... more Eukaryotic gene fusion and fission events are mechanistically more complicated than in prokaryotes, and their quantitative contributions to genome evolution are still poorly understood. We have identified all differentially composite or split genes in 2 fully sequenced plant genomes, Oryza sativa and Arabidopsis thaliana. Out of 10,172 orthologous gene pairs, 60 (0.6% of the total) revealed a verified fusion or fission event in either lineage after the divergence of O. sativa and A. thaliana. Polarizing these events by outgroup comparison revealed differences in the rate of gene fission but not of gene fusion in the rice and Arabidopsis lineages. Gene fission occurred at a higher rate than gene fusion in the O. sativa lineage and was furthermore more common in rice than in Arabidopsis. Nucleotide insertion bias has promoted gene fission in the O. sativa lineage, consistent with its generally longer nucleotide sequences than A. thaliana in selectively neutral regions, and with the abundance of transposable elements in rice. The divergence time of monocots and dicots (140-200 Myr) indicates that gene fusion/fission events occur at an average rate of 1 3 10 À11 to 2 3 10 À11 events per gene per year, ;100fold slower than the average per site nuclear nucleotide substitution rate in these lineages. Gene fusion and fission are thus rare and slow processes in higher plant genomes; they should be of utility to address deeper evolutionary relationships among plants-and the relationship of plants to other eukaryotic lineages-where sequence-based phylogenies provide equivocal or conflicting results. Recently, the genome sequence of rice, Oryza sativa (O. sativa L. ssp. japonica cv. Nipponbare), has been determined. Its gene repertoire was quite thoroughly annotated using full-length cDNA libraries (International Rice Genome Sequencing Project 2005; Ohyanagi et al. 2006). This permits a monocot-dicot comparison to the Arabidopsis thaliana genome (Arabidopsis Genome Initiative 2000). Here, we addressed the evolutionary dynamics of gene fusion and fission events in these plant genomes. We identify all of the candidates of gene fusion or fission events, which have occurred after the divergence of O. sativa and A. thaliana. We report the number and rate of the events including all genes and coordinates involved as well as their functional annotations and reconstruct the evolutionary scenario of differential gene fusion and fission in each lineage. Materials and Methods Protein Sequences in O. sativa and A. thaliana We collected a total of 40,041 protein sequences in O. sativa genomes annotated in the Rice Annotation Project (RAP) as of 14 June 2005 (Ohyanagi et al. 2006) and 28,860 protein sequences in A. thaliana in GenBank. We then checked the locations of protein-coding genes on genomes and whether their overlap was due to alternative splicing or redundant annotation, using longer ones if locations overlapped. This yielded a total of 28,759 protein sequences from O. sativa and 26,364 sequences from A. thaliana. Among those O. sativa sequences, 21,818 are supported by full-length cDNA in RAP. To check the A. thaliana sequences, we downloaded 15,295 full-length cDNA records as of 24 May 2005 from RIKEN ftp site (http:// rarge.gsc.riken.jp/archives/rafl/sequence/) and confirmed
Geochimica et Cosmochimica Acta, 1989
Aktnct-Organic carbon oxidation rates in San Clemente Besin wm &term&d by benthic chamber experim... more Aktnct-Organic carbon oxidation rates in San Clemente Besin wm &term&d by benthic chamber experiments using the Bottom Lander, along with studies of pore water chemi&y. Non-steady-state diagenetic models are developed for interp&ng concentration-time data from the benthic chamber experiments. 4, NOi, and a-81~ all important oxidsnts for orgsnic carbon at our study site. Regenerated fixed nitrogen WBS consumed by NO; reduction. Ikerr is a tlux of NO j into the sediments, and the benthic flux of NHt is undetectable. The total rate at which fixed nitrogen is removal from the oceans at this she is about twice the flux of PON to the sea floor. Si@ fluxes calculated from interfacial pore water gradients are in satisfactory agreement with those determined using the Lander. Most sika dissolution must therefore occur within the sediment.% although interstitial profiles show that little dkolution occurs below I cm depth. INTRODUCIION A UNIFIED VIEW of early diageneais in pelagic sediments has developed over the last decade. Sedimentary organic carbon is oxidized Jequentially by 02, NO;, MnOz, Fe203 and SO$-. The order reflects the free energy of C, oxidation, and is manifested by a characteristic pattern of depth variability in pore water concentrations of 02, NO;, Mn2+, Fti+, a-, TA (total alkalinity), TCOZ (total a), and other species (FROEUCH et al., 1979; EMERSON er al., 1980, and otbers). Concentrations of these variables covary in ways &Ming the stoichiometry of the G degradation dons (SHOL
Geobiology, 2010
For life to have emerged from CO 2 , rocks, and water on the early Earth, a sustained source of c... more For life to have emerged from CO 2 , rocks, and water on the early Earth, a sustained source of chemically transducible energy was essential. The serpentinization process is emerging as an increasingly likely source of that energy. Serpentinization of ultramafic crust would have continuously supplied hydrogen, methane, minor formate, and ammonia, as well as calcium and traces of acetate, molybdenum and tungsten, to off-ridge alkaline hydrothermal springs that interfaced with the metal-rich carbonic Hadean Ocean. Silica and bisulfide were also delivered to these springs where cherts and sulfides were intersected by the alkaline solutions. The proton and redox gradients so generated represent a rich source of naturally produced chemiosmotic energy, stemming from geochemistry that merely had to be tapped, rather than induced, by the earliest biochemical systems. Hydrothermal mounds accumulating at similar sites in today's oceans offer conceptual and experimental models for the chemistry germane to the emergence of life, although the ubiquity of microbial communities at such sites in addition to our oxygenated atmosphere preclude an exact analogy.