Papers by William Whitman
BMC Genomics, 2009
Background: Staphylothermus marinus is an anaerobic, sulfur-reducing peptide fermenter of the arc... more Background: Staphylothermus marinus is an anaerobic, sulfur-reducing peptide fermenter of the archaeal phylum Crenarchaeota. It is the third heterotrophic, obligate sulfur reducing crenarchaeote to be sequenced and provides an opportunity for comparative analysis of the three genomes. Results: The 1.57 Mbp genome of the hyperthermophilic crenarchaeote Staphylothermus marinus has been completely sequenced. The main energy generating pathways likely involve 2oxoacid:ferredoxin oxidoreductases and ADP-forming acetyl-CoA synthases. S. marinus possesses several enzymes not present in other crenarchaeotes including a sodium ion-translocating decarboxylase likely to be involved in amino acid degradation. S. marinus lacks sulfur-reducing enzymes present in the other two sulfur-reducing crenarchaeotes that have been sequenced -Thermofilum pendens and Hyperthermus butylicus. Instead it has three operons similar to the mbh and mbx operons of Pyrococcus furiosus, which may play a role in sulfur reduction and/or hydrogen
Journal of Bacteriology, Oct 1, 1983
Applied and Environmental Microbiology, May 1, 1988
Nature microbiology, Jun 21, 2021
An increasing wealth of genomic data from cultured and uncultured microorganisms provides the opp... more An increasing wealth of genomic data from cultured and uncultured microorganisms provides the opportunity to develop a systematic taxonomy based on evolutionary relationships. Here we propose a standardized archaeal taxonomy, as part of the Genome Taxonomy Database (GTDB), derived from a 122 concatenated protein phylogeny that resolves polyphyletic groups and normalizes ranks based on relative evolutionary divergence (RED). The resulting archaeal taxonomy is stable under a range of phylogenetic variables, including marker genes, inference methods, corrections for rate heterogeneity and compositional bias, tree rooting scenarios, and expansion of the genome database. Rank normalization was shown to robustly correct for substitution rates varying up to 30-fold using simulated datasets. Taxonomic curation follows the rules of the International Code of Nomenclature of Prokaryotes (ICNP) while taking into account proposals to formally recognise the rank of phylum and to use genome sequences as type material. The taxonomy is based on 2,392 quality screened archaeal genomes, the great majority of which (93.3%) required one or more changes to their existing taxonomy, mostly as a result of incomplete classification. In total, 16 archaeal phyla are described, including reclassification of three major monophyletic units from the former Euryarchaeota and one phylum resulting from uniting the TACK superphylum into a single phylum. The taxonomy is publicly available at the GTDB website (). Carl Woese's discovery of the Archaea in 1977, originally termed Archaebacteria gave rise to the recognition of a new domain of life and fundamentally changed our view of cellular evolution .
Microbiology Resource Announcements, 2021
Here, we announce the genomes of eight Roseibium album (synonym Labrenzia alba ) strains that wer... more Here, we announce the genomes of eight Roseibium album (synonym Labrenzia alba ) strains that were obtained from the octocoral Eunicella labiata . Genome annotation revealed multiple symbiosis factors common to all genomes, such as eukaryotic-like repeat protein- and multidrug resistance-encoding genes, which likely underpin symbiotic relationships with marine invertebrate hosts.
International Journal of Systematic and Evolutionary Microbiology, 1999
Journal of Bacteriology, 1989
Small amounts of a 23-kilobase covalently closed circular DNA molecule were isolated from unwashe... more Small amounts of a 23-kilobase covalently closed circular DNA molecule were isolated from unwashed cells of Methanococcus voltae A3. Further investigation indicated the presence of greater quantities of the circular DNA in the culture supernatant, complexed with protein in a manner rendering the DNA resistant to DNase. Electron-microscopic examination of supernatant material revealed the presence of particles which morphologically resemble virus. Phenol extraction of viruslike particle preparations resulted in the recovery of DNase-sensitive open-circular DNA molecules. As many as 30 viruslike particles per cell were recovered from some cultures. Hybridization data clearly indicated the presence of a chromosomally integrated copy of the viruslike particle DNA. Although M. voltae PS was not observed to produce viruslike particles, DNA homologous to the viruslike particle DNA was detected in its chromosome. A mutant of M. voltae A3 was isolated which produced no particles; its DNA was...
Standards in Genomic Sciences, 2009
Methanocorpusculum labreanum is a methanogen belonging to the order Methanomicrobiales within the... more Methanocorpusculum labreanum is a methanogen belonging to the order Methanomicrobiales within the archaeal phylum Euryarchaeota. The type strain Z was isolated from surface sediments of Tar Pit Lake in the La Brea Tar Pits in Los Angeles, California. M. labreanum is of phylogenetic interest because at the time the sequencing project began only one genome had previously been sequenced from the order Methanomicrobiales. We report here the complete genome sequence of M. labreanum type strain Z and its annotation. This is part of a 2006 Joint Genome Institute Community Sequencing Program project to sequence genomes of diverse Archaea.
Journal of Biological Chemistry, 2010
Three multiprotein systems are known for iron-sulfur (Fe-S) cluster biogenesis in prokaryotes and... more Three multiprotein systems are known for iron-sulfur (Fe-S) cluster biogenesis in prokaryotes and eukaryotes as follows: the NIF (nitrogen fixation), the ISC (iron-sulfur cluster), and the SUF (mobilization of sulfur) systems. In all three, cysteine is the physiological sulfur source, and the sulfur is transferred from cysteine desulfurase through a persulfidic intermediate to a scaffold protein. However, the biochemical nature of the sulfur source for Fe-S cluster assembly in archaea is unknown, and many archaea lack homologs of cysteine desulfurases. Methanococcus maripaludis is a methanogenic archaeon that contains a high amount of protein-bound Fe-S clusters (45 nmol/mg protein). Cysteine in this archaeon is synthesized primarily via the tRNA-dependent SepRS/SepCysS pathway. When a ⌬sepS mutant (a cysteine auxotroph) was grown with 34 S-labeled sulfide and unlabeled cysteine, <8% of the cysteine, >92% of the methionine, and >87% of the sulfur in the Fe-S clusters in proteins were labeled, suggesting that the sulfur in methionine and Fe-S clusters was derived predominantly from exogenous sulfide instead of cysteine. Therefore, this investigation challenges the concept that cysteine is always the sulfur source for Fe-S cluster biosynthesis in vivo and suggests that Fe-S clusters are derived from sulfide in those organisms, which live in sulfiderich habitats.
Journal of Bacteriology, 2008
We report the complete genome of Thermofilum pendens , a deeply branching, hyperthermophilic memb... more We report the complete genome of Thermofilum pendens , a deeply branching, hyperthermophilic member of the order Thermoproteales in the archaeal kingdom Crenarchaeota. T. pendens is a sulfur-dependent, anaerobic heterotroph isolated from a solfatara in Iceland. It is an extracellular commensal, requiring an extract of Thermoproteus tenax for growth, and the genome sequence reveals that biosynthetic pathways for purines, most amino acids, and most cofactors are absent. In fact, T. pendens has fewer biosynthetic enzymes than obligate intracellular parasites, although it does not display other features that are common among obligate parasites and thus does not appear to be in the process of becoming a parasite. It appears that T. pendens has adapted to life in an environment rich in nutrients. T. pendens was known previously to utilize peptides as an energy source, but the genome revealed a substantial ability to grow on carbohydrates. T. pendens is the first crenarchaeote and only the...
Journal of Bacteriology, Aug 1, 2010
The Methanococcus maripaludis energy-conserving hydrogenase B (Ehb) generates low potential elect... more The Methanococcus maripaludis energy-conserving hydrogenase B (Ehb) generates low potential electrons required for autotrophic CO 2 assimilation. To analyze the importance of individual subunits in Ehb structure and function, markerless in-frame deletions were constructed in a number of M. maripaludis ehb genes. These genes encode the large and small hydrogenase subunits (ehbN and ehbM, respectively), a polyferredoxin and ferredoxin (ehbK and ehbL, respectively), and an ion translocator (ehbF). In addition, a gene replacement mutation was constructed for a gene encoding a putative membrane-spanning subunit (ehbO). When grown in minimal medium plus acetate (McA), all ehb mutants had severe growth deficiencies except the ⌬ehbO::pac strain. The membrane-spanning ion translocator (⌬ehbF) and the large hydrogenase subunit (⌬ehbN) deletion strains displayed the severest growth defects. Deletion of the ehbN gene was of particular interest because this gene was not contiguous to the ehb operon. In-gel activity assays and Western blots confirmed that EhbN was part of the membrane-bound Ehb hydrogenase complex. The ⌬ehbN strain was also sensitive to growth inhibition by aryl acids, indicating that Ehb was coupled to the indolepyruvate oxidoreductase (Ior), further supporting the hypothesis that Ehb provides low potential reductants for the anabolic oxidoreductases in M. maripaludis.
Standards in Genomic Sciences, Dec 17, 2013
Pedobiologia, Nov 1, 2005
Soils are the centrai organizing entities in terrestrial ecosystem and possess extremely diverse ... more Soils are the centrai organizing entities in terrestrial ecosystem and possess extremely diverse prokaryotic and eukaryotic biota. They are physically and chemically complex, with micro-and macro-aggregates embedded within a solid, liquid and gaseous matrix that is continually changing in response to natural and human-induced perturbations. Recent advances in mdecu tar techniques in systematics have provided opportunities for the study of biodiversity and biocomplexiay of soit biota. A symposium and workshop on soit biogeochemistry and biodiversity international Symposium on Impacts of Soil Biodiversity on Biogeochemicat Processes in Ecosystems, Taiwan Forestry Research Institute, Taipei, Taiwan April 18-24, 2004. Convened an international array of participants working in biomes on virtually every continent on the planet (ranging from polar to tropical rqions). This special issue reports on the theoretical bases anct applications of molecular methods for the measurement of soil biodiversity. Themes addressed inctude a melding of classical taxonomic investigations with biochemical fingerprinting and molecutar probing of organism identities. Several papers highlight new advances in identifications of prokaryotic and eukaryotic organisms. Examples include new developments in "fingerprinting" of microbes active in * C m w n~ author.
Standards in Genomic Sciences, May 17, 2015
The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was launched by the JGI in 2007 a... more The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was launched by the JGI in 2007 as a pilot project to sequence about 250 bacterial and archaeal genomes of elevated phylogenetic diversity. Herein, we propose to extend this approach to type strains of prokaryotes associated with soil or plants and their close relatives as well as type strains from newly described species. Understanding the microbiology of soil and plants is critical to many DOE mission areas, such as biofuel production from biomass, biogeochemistry, and carbon cycling. We are also targeting type strains of novel species while they are being described. Since 2006, about 630 new species have been described per year, many of which are closely aligned to DOE areas of interest in soil, agriculture, degradation of pollutants, biofuel production, biogeochemical transformation, and biodiversity.
Communications Biology
Methanogens and anaerobic methane-oxidizing archaea (ANME) are important players in the global ca... more Methanogens and anaerobic methane-oxidizing archaea (ANME) are important players in the global carbon cycle. Methyl-coenzyme M reductase (MCR) is a key enzyme in methane metabolism, catalyzing the last step in methanogenesis and the first step in anaerobic methane oxidation. Divergent mcr and mcr-like genes have recently been identified in uncultured archaeal lineages. However, the assembly and biochemistry of MCRs from uncultured archaea remain largely unknown. Here we present an approach to study MCRs from uncultured archaea by heterologous expression in a methanogen, Methanococcus maripaludis. Promoter, operon structure, and temperature were important determinants for MCR production. Both recombinant methanococcal and ANME-2 MCR assembled with the host MCR forming hybrid complexes, whereas tested ANME-1 MCR and ethyl-coenzyme M reductase only formed homogenous complexes. Together with structural modeling, this suggests that ANME-2 and methanogen MCRs are structurally similar and ...
Genetics, 1999
To learn more about autotrophic growth of methanococci, we isolated nine conditional mutants of M... more To learn more about autotrophic growth of methanococci, we isolated nine conditional mutants of Methanococcus maripaludis after transformation of the wild type with a random library in pMEB.2, a suicide plasmid bearing the puromycin-resistance cassette pac. These mutants grew poorly in mineral medium and required acetate or complex organic supplements such as yeast extract for normal growth. One mutant, JJ104, was a leaky acetate auxotroph. A plasmid, pWDK104, was recovered from this mutant by electroporation of a plasmid preparation into Escherichia coli. Transformation of wild-type M. maripaludis with pWDK104 produced JJ104-1, a mutant with the same phenotype as JJ104, thus establishing that insertion of pWDK104 into the genome was responsible for the phenotype. pWDK104 contained portions of the methanococcal genes encoding an ABC transporter closely related to MJ1367-MJ1368 of M. jannaschii. Because high levels of molybdate, tungstate, and selenite restored growth to wild-type le...
Frontiers in Microbiology, 2021
Taxonomic decisions within the order Rhizobiales have relied heavily on the interpretations of hi... more Taxonomic decisions within the order Rhizobiales have relied heavily on the interpretations of highly conserved 16S rRNA sequences and DNA–DNA hybridizations (DDH). Currently, bacterial species are defined as including strains that present 95–96% of average nucleotide identity (ANI) and 70% of digital DDH (dDDH). Thus, ANI values from 520 genome sequences of type strains from species of Rhizobiales order were computed. From the resulting 270,400 comparisons, a ≥95% cut-off was used to extract high identity genome clusters through enumerating maximal cliques. Coupling this graph-based approach with dDDH from clusters of interest, it was found that: (i) there are synonymy between Aminobacter lissarensis and Aminobacter carboxidus, Aurantimonas manganoxydans and Aurantimonas coralicida, “Bartonella mastomydis,” and Bartonella elizabethae, Chelativorans oligotrophicus, and Chelativorans multitrophicus, Rhizobium azibense, and Rhizobium gallicum, Rhizobium fabae, and Rhizobium pisi, and ...
Microbiological Reviews, 1987
TABLE 1. Summary of characteristics of methanogenic archaebacteria, order Methanobacterialesa Tem... more TABLE 1. Summary of characteristics of methanogenic archaebacteria, order Methanobacterialesa Temp p Archaebacteria Morphology Substrates G+C optimum pH Cell envelope Major membrane Reference(s) (mol%) (OC) optimum composition isoprenoid Family Methanobacteriaceae Methanobacterium formicicum Rod H2, formate 40.7 7.0 Pseudomurein C20 + C40 12 M. bryantii Rod H2 32.7 38 7.0 Pseudomurein C20 + C40 12 M. thermoautotrophicum Rod H,
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Papers by William Whitman