Multi-omics analysis provides insight to the Ignicoccus hospitalis - Nanoarchaeum equitans association

Rawle, Rachel A.; Hamerly, Timothy; Tripet, Brian P.; Giannone, Richard J.; Wurch, Louie; Hettich, Robert L.; Podar, Mircea; Copié, Valerie; Bothner, Brian

doi:10.1016/j.bbagen.2017.06.001

Multi-omics analysis provides insight to the Ignicoccus hospitalis - Nanoarchaeum equitans association

Journal Article · Sun Jun 04 00:00:00 EDT 2017 · Biochimica et Biophysica Acta - General Subjects

DOI:https://doi.org/10.1016/j.bbagen.2017.06.001· OSTI ID:1400161

Rawle, Rachel A. ^[1]; Hamerly, Timothy ^[2]; Tripet, Brian P. ^[2]; Giannone, Richard J. ^[3]; Wurch, Louie ^[4]; Hettich, Robert L. ^[3]; Podar, Mircea ^[4]; Copié, Valerie ^[5]; Bothner, Brian ^[5]

Montana State Univ., Bozeman, MT (United States). Dept. of Microbiology; Montana State Univ., Bozeman, MT (United States). Dept. of Chemistry and Biochemistry
Montana State Univ., Bozeman, MT (United States). Dept. of Chemistry and Biochemistry
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States). Dept. of Microbiology
Montana State Univ., Bozeman, MT (United States). Dept. of Chemistry and Biochemistry; Montana State Univ., Bozeman, MT (United States). Thermal Biology Inst.

Studies of interspecies interactions are inherently difficult due to the complex mechanisms which enable these relationships. A model system for studying interspecies interactions is the marine hyperthermophiles Ignicoccus hospitalis and Nanoarchaeum equitans. Recent independently-conducted ‘omics’ analyses have generated insights into the molecular factors modulating this association. However, significant questions remain about the nature of the interactions between these archaea. We jointly analyzed multiple levels of omics datasets obtained from published, independent transcriptomics, proteomics, and metabolomics analyses. DAVID identified functionally-related groups enriched when I. hospitalis is grown alone or in co-culture with N. equitans. Enriched molecular pathways were subsequently visualized using interaction maps generated using STRING. Key findings of our multi-level omics analysis indicated that I. hospitalis provides precursors to N. equitans for energy metabolism. Analysis indicated an overall reduction in diversity of metabolic precursors in the I. hospitalis–N. equitans co-culture, which has been connected to the differential use of ribosomal subunits and was previously unnoticed. We also identified differences in precursors linked to amino acid metabolism, NADH metabolism, and carbon fixation, providing new insights into the metabolic adaptions of I. hospitalis enabling the growth of N. equitans. In conclusion, this multi-omics analysis builds upon previously identified cellular patterns while offering new insights into mechanisms that enable the I. hospitalis–N. equitans association. This study applies statistical and visualization techniques to a mixed-source omics dataset to yield a more global insight into a complex system, that was not readily discernable from separate omics studies.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: National Science Foundation (NSF); USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC05-00OR22725; SC0006654

OSTI ID:: 1400161

Alternate ID(s):: OSTI ID: 1550118

Journal Information:: Biochimica et Biophysica Acta - General Subjects, Journal Name: Biochimica et Biophysica Acta - General Subjects Journal Issue: 9 Vol. 1861; ISSN 0304-4165

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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