Genomic analysis of the uncultivated marine crenarchaeote
            <i>Cenarchaeum symbiosum</i>

Hallam, Steven J.; Konstantinidis, Konstantinos; Putnam, Nicholas H.; Schleper, Christa; Watanabe, Yoh-ichi; Sugahara, Junichi; Preston, Christina M.; Torre, José de la; Richardson, Paul M.; DeLong, Edward F.

doi:10.1073/pnas.0608549103

Cited by 423 publications

(396 citation statements)

References 55 publications

Supporting

Mentioning

372

Contrasting

Unclassified

Order By: Relevance

“…In order to identify the amino acid residues involved in catalysis and/or substrate recognition, we searched for highly conserved residues by aligning the amino acid sequences of 27 PoK protein homologs from diverse archaeal species. We found that the PoK homologs are present in the recently sequenced genomes of Thaumarchaeota Cenarchaeum symbiosum (8) and Nitrosopumilus maritimus (31). The alignment with nine representative sequences is shown in Fig.…”

Section: Production and Purification Of Recombinant Pantoate Kinasementioning

confidence: 96%

Biochemical Characterization of Pantoate Kinase, a Novel Enzyme Necessary for Coenzyme A Biosynthesis in the Archaea

et al. 2012

View full text Add to dashboard Cite

Although bacteria and eukaryotes share a pathway for coenzyme A (CoA) biosynthesis, we previously clarified that most archaea utilize a distinct pathway for the conversion of pantoate to 4=-phosphopantothenate. Whereas bacteria/eukaryotes use pantothenate synthetase and pantothenate kinase (PanK), the hyperthermophilic archaeon Thermococcus kodakarensis utilizes two novel enzymes: pantoate kinase (PoK) and phosphopantothenate synthetase (PPS). Here, we report a detailed biochemical examination of PoK from T. kodakarensis. Kinetic analyses revealed that the PoK reaction displayed Michaelis-Menten kinetics toward ATP, whereas substrate inhibition was observed with pantoate. PoK activity was not affected by the addition of CoA/acetyl-CoA. Interestingly, PoK displayed broad nucleotide specificity and utilized ATP, GTP, UTP, and CTP with comparable k cat /K m values. Sequence alignment of 27 PoK homologs revealed seven conserved residues with reactive side chains, and variant proteins were constructed for each residue. Activity was not detected when mutations were introduced to Ser104, Glu134, and Asp143, suggesting that these residues play vital roles in PoK catalysis. Kinetic analysis of the other variant proteins, with mutations S28A, H131A, R155A, and T186A, indicated that all four residues are involved in pantoate recognition and that Arg155 and Thr186 play important roles in PoK catalysis. Gel filtration analyses of the variant proteins indicated that Thr186 is also involved in dimer assembly. A sequence comparison between PoK and other members of the GHMP kinase family suggests that Ser104 and Glu134 are involved in binding with phosphate and Mg 2؉ , respectively, while Asp143 is the base responsible for proton abstraction from the pantoate hydroxy group.

show abstract

Section: Production and Purification Of Recombinant Pantoate Kinasementioning

confidence: 96%

Biochemical Characterization of Pantoate Kinase, a Novel Enzyme Necessary for Coenzyme A Biosynthesis in the Archaea

et al. 2012

View full text Add to dashboard Cite

show abstract

“…Owing to the nature of the samples and the algorithms used, assembly can produce chimeric contigs and scaffolds comprising reads from different organisms. Strain heterogeneity can add considerably to this problem as the probability of co-assembly increases with closely related genomes 4 .…”

mentioning

confidence: 99%

Use of simulated data sets to evaluate the fidelity of metagenomic processing methods

et al. 2007

View full text Add to dashboard Cite

Metagenomics is a rapidly emerging field of research for studying microbial communities. To evaluate methods presently used to process metagenomic sequences, we constructed three simulated data sets of varying complexity by combining sequencing reads randomly selected from 113 isolate genomes. These data sets were designed to model real metagenomes in terms of complexity and phylogenetic composition. We assembled sampled reads using three commonly used genome assemblers (Phrap, Arachne and JAZZ), and predicted genes using two popular gene finding pipelines (fgenesb and CRITICA/GLIMMER). The phylogenetic origins of the assembled contigs were predicted using one sequence similarity-based (blast hit distribution) and two sequence composition-based (PhyloPythia, oligonucleotide frequencies) binning methods. We explored the effects of the simulated community structure and method combinations on the fidelity of each processing step by comparison to the corresponding isolate genomes. The simulated data sets are available online to facilitate standardized benchmarking of tools for metagenomic analysis.Recent advances in sequencing technology are mediating a transition from organismal to community genomics (metagenomics), allowing us to directly examine the molecular blueprints of microbial communities. Metagenomic data processing follows essentially the same steps as processing of shotgun sequences generated for isolate genomes, starting with the assembly of sequence reads, followed by gene prediction and functional annotation. The genome sequence of an isolated microorganism, however, is typically derived from a clonal population, whereas metagenomic projects sample the genomes of multiple species and strains present in highly variable abundance in a microbial community. Quality control steps that detect assembly and gene-finding errors, such as finishing and gap closure, or manual curation of genes and functions, are mostly omitted. The final output of this process is similar to that

show abstract

“…Both come from shallow waters, the sponge symbiont Cenarchaeum symbiosum (Hallam et al, 2006) and the aquarium isolate N. maritimus (Walker et al, 2010). Recently, draft genome sequence has been obtained from single cells and San Francisco Bay sediment enrichments of Nitrosoarchaeum limnia, recovered from an estuary in San Francisco bay (Blainey et al, 2011) and from a soil isolate, Nitrososphaera viennensis (Tourna et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Genome-enabled transcriptomics reveals archaeal populations that drive nitrification in a deep-sea hydrothermal plume

2012

View full text Add to dashboard Cite

Ammonia-oxidizing Archaea (AOA) are among the most abundant microorganisms in the oceans and have crucial roles in biogeochemical cycling of nitrogen and carbon. To better understand AOA inhabiting the deep sea, we obtained community genomic and transcriptomic data from ammonium-rich hydrothermal plumes in the Guaymas Basin (GB) and from surrounding deep waters of the Gulf of California. Among the most abundant and active lineages in the sequence data were marine group I (MGI) Archaea related to the cultured autotrophic ammonia-oxidizer, Nitrosopumilus maritimus. Assembly of MGI genomic fragments yielded 2.9 Mb of sequence containing seven 16S rRNA genes (95.4–98.4% similar to N. maritimus), including two near-complete genomes and several lower-abundance variants. Equal copy numbers of MGI 16S rRNA genes and ammonia monooxygenase genes and transcription of ammonia oxidation genes indicates that all of these genotypes actively oxidize ammonia. De novo genomic assembly revealed the functional potential of MGI populations and enhanced interpretation of metatranscriptomic data. Physiological distinction from N. maritimus is evident in the transcription of novel genes, including genes for urea utilization, suggesting an alternative source of ammonia. We were also able to determine which genotypes are most active in the plume. Transcripts involved in nitrification were more prominent in the plume and were among the most abundant transcripts in the community. These unique data sets reveal populations of deep-sea AOA thriving in the ammonium-rich GB that are related to surface types, but with key genomic and physiological differences.

show abstract

Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum

Cited by 423 publications

References 55 publications

Biochemical Characterization of Pantoate Kinase, a Novel Enzyme Necessary for Coenzyme A Biosynthesis in the Archaea

Biochemical Characterization of Pantoate Kinase, a Novel Enzyme Necessary for Coenzyme A Biosynthesis in the Archaea

Use of simulated data sets to evaluate the fidelity of metagenomic processing methods

Genome-enabled transcriptomics reveals archaeal populations that drive nitrification in a deep-sea hydrothermal plume

Contact Info

Product

Resources

About