Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea

Makarova, Kira S.; Sorokin, Alexander V.; Novichkov, Pavel S.; Wolf, Yuri I.; Koonin, Eugene V.

doi:10.1186/1745-6150-2-33

Cited by 163 publications

(212 citation statements)

References 81 publications

(62 reference statements)

Supporting

Mentioning

192

Contrasting

Order By: Relevance

“…No unambiguous origin of replication could be determined on the basis of local gene content or GC skew, as commonly observed for other archaeal genomes (14). Approximately 61% of the N. maritimus open-reading frames (ORFs) could be assigned to clusters of orthologous groups of proteins (COGs), a lower percentage than for genomes of ammonia-oxidizing bacteria (AOB) ( Table S1) but similar to Cenarchaeum symbiosum (15). The genome possesses a relatively high coding density (91.9%), with a larger fraction dedicated to energy production/conservation, coenzyme transport/metabolism, and translation genes than other characterized Crenarchaeota, but similar to two common species of photoautotrophic marine Bacteria, Prochlorococcus, and Synechococcus.…”

Section: Resultsmentioning

confidence: 99%

Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea

Walker

Torre

Klotz

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

854

894

View full text Add to dashboard Cite

Ammonia-oxidizing archaea are ubiquitous in marine and terrestrial environments and now thought to be significant contributors to carbon and nitrogen cycling. The isolation of Candidatus “ Nitrosopumilus maritimus ” strain SCM1 provided the opportunity for linking its chemolithotrophic physiology with a genomic inventory of the globally distributed archaea. Here we report the 1,645,259-bp closed genome of strain SCM1, revealing highly copper-dependent systems for ammonia oxidation and electron transport that are distinctly different from known ammonia-oxidizing bacteria. Consistent with in situ isotopic studies of marine archaea, the genome sequence indicates N. maritimus grows autotrophically using a variant of the 3-hydroxypropionate/4-hydroxybutryrate pathway for carbon assimilation, while maintaining limited capacity for assimilation of organic carbon. This unique instance of archaeal biosynthesis of the osmoprotectant ectoine and an unprecedented enrichment of multicopper oxidases, thioredoxin-like proteins, and transcriptional regulators points to an organism responsive to environmental cues and adapted to handling reactive copper and nitrogen species that likely derive from its distinctive biochemistry. The conservation of N. maritimus gene content and organization within marine metagenomes indicates that the unique physiology of these specialized oligophiles may play a significant role in the biogeochemical cycles of carbon and nitrogen.

show abstract

Section: Resultsmentioning

confidence: 99%

Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea

Walker

Torre

Klotz

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

854

894

View full text Add to dashboard Cite

show abstract

“…The applied gel-and enrichment-free PAcIFIC (precursor acquisition independent from ion count) approach (438) revealed an unexpectedly large number of phosphoproteins (540 phosphoproteins) as well as a large amount of p-Tyr (54%) (439). The identified phosphoproteins are located in 21 out of 26 arCOG categories (440), indicating that most of the cellular processes are targeted by protein phosphorylation. For Sul.…”

Section: Regulation At the Protein Levelmentioning

confidence: 99%

“…Furthermore, the identified percent pS/T/Y ratio is unique regarding the amount of p-Tyr (54%) compared to those reported for other phosphoproteome studies (1 to 10%). It was shown that the identified phosphoproteins are located in 21 out of 26 arCOG categories (440), indicating that most of the cellular processes are targeted by protein phosphorylation. In response to the offered carbon source, significant changes in the complex phosphorylation pattern were observed, suggesting an important physiological function of reversible protein phosphorylation in the control of central carbohydrate metabolism.…”

Section: Sulfolobus Solfataricusmentioning

confidence: 99%

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Bräsen

Esser

Rauch

et al. 2014

Microbiol Mol Biol Rev

271

294

View full text Add to dashboard Cite

SUMMARY The metabolism of Archaea , the third domain of life, resembles in its complexity those of Bacteria and lower Eukarya . However, this metabolic complexity in Archaea is accompanied by the absence of many “classical” pathways, particularly in central carbohydrate metabolism. Instead, Archaea are characterized by the presence of unique, modified variants of classical pathways such as the Embden-Meyerhof-Parnas (EMP) pathway and the Entner-Doudoroff (ED) pathway. The pentose phosphate pathway is only partly present (if at all), and pentose degradation also significantly differs from that known for bacterial model organisms. These modifications are accompanied by the invention of “new,” unusual enzymes which cause fundamental consequences for the underlying regulatory principles, and classical allosteric regulation sites well established in Bacteria and Eukarya are lost. The aim of this review is to present the current understanding of central carbohydrate metabolic pathways and their regulation in Archaea . In order to give an overview of their complexity, pathway modifications are discussed with respect to unusual archaeal biocatalysts, their structural and mechanistic characteristics, and their regulatory properties in comparison to their classic counterparts from Bacteria and Eukarya . Furthermore, an overview focusing on hexose metabolic, i.e., glycolytic as well as gluconeogenic, pathways identified in archaeal model organisms is given. Their energy gain is discussed, and new insights into different levels of regulation that have been observed so far, including the transcript and protein levels (e.g., gene regulation, known transcription regulators, and posttranslational modification via reversible protein phosphorylation), are presented.

show abstract

“…The increasing availability of sequence information from diverse organisms has allowed the application of comparative genomics, or phylogenomics, to discover proteins specific to bacteria (10 -12), cyanobacteria (13)(14)(15), fungi (16,17), metazoa (18), archaea (19), and plastids (20). Additionally, computational attempts have been made to recognize protein families that are conserved in select plant genomes (21).…”

mentioning

confidence: 99%

The GreenCut2 Resource, a Phylogenomically Derived Inventory of Proteins Specific to the Plant Lineage

Karpowicz

Prochnik

Grossman

et al. 2011

Journal of Biological Chemistry

121

152

View full text Add to dashboard Cite

The plastid is a defining structure of photosynthetic eukaryotes and houses many plant-specific processes, including the light reactions, carbon fixation, pigment synthesis, and other primary metabolic processes. Identifying proteins associated with catalytic, structural, and regulatory functions that are unique to plastid-containing organisms is necessary to fully define the scope of plant biochemistry. Here, we performed phylogenomics on 20 genomes to compile a new inventory of 597 nucleus-encoded proteins conserved in plants and green algae but not in non-photosynthetic organisms. 286 of these proteins are of known function, whereas 311 are not characterized. This inventory was validated as applicable and relevant to diverse photosynthetic eukaryotes using an additional eight genomes from distantly related plants (including Micromonas, Selaginella, and soybean). Manual curation of the known proteins in the inventory established its importance to plastid biochemistry. To predict functions for the 52% of proteins of unknown function, we used sequence motifs, subcellular localization, co-expression analysis, and RNA abundance data. We demonstrate that 18% of the proteins in the inventory have functions outside the plastid and/or beyond green tissues. Although 32% of proteins in the inventory have homologs in all cyanobacteria, unexpectedly, 30% are eukaryote-specific. Finally, 8% of the proteins of unknown function share no similarity to any characterized protein and are plant lineage-specific. We present this annotated inventory of 597 proteins as a resource for functional analyses of plant-specific biochemistry.The plastid is an organelle in plants and algae that evolved from a photosynthetic cyanobacterium after it was engulfed by an ancestral eukaryotic cell over 1.5 billion years ago (1, 2). How the endosymbiont became integral to host cell functions and evolved into a plastid is still under debate (3), but functions localized to the present day plastid depend on both plastid-and nucleus-encoded proteins. The latter are synthesized in the cytoplasm and imported into the organelle by a specific multiprotein complex composed of the translocon of the outer and inner chloroplast envelope membrane (TOC 4 and TIC, respectively) proteins (4, 5). Over 2000 proteins are estimated to be located in the plastid with the vast majority (Ͼ90%) encoded by genes in the nucleus (6 -9). Many of the nucleus-encoded proteins that function within plastids are conserved among photosynthetic organisms. These conserved proteins function in processes such as the capture and utilization of excitation energy, carbohydrate metabolism, and the synthesis of key cellular metabolites (such as lipids, isoprenoids, pigments, and amino acids). Interestingly, however, many plastid-localized proteins have not yet been assigned a specific biochemical function.The increasing availability of sequence information from diverse organisms has allowed the application of comparative genomics, or phylogenomics, to discover proteins specific to bacteria (...

show abstract

Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea

Cited by 163 publications

References 81 publications

Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea

Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

The GreenCut2 Resource, a Phylogenomically Derived Inventory of Proteins Specific to the Plant Lineage

Contact Info

Product

Resources

About