Development of an Ocean Protein Portal for Interactive Discovery and Education

Saito, Mak A.; Saunders, Jaclyn K.; Chagnon, Michael; Gaylord, David A.; Shepherd, Adam; Held, Noelle A.; Dupont, Christopher L.; Symmonds, Nicholas; York, Amber; Charron, Matthew; Kinkade, Danie

doi:10.1021/acs.jproteome.0c00382

Cited by 11 publications

(13 citation statements)

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“…With the natural environment undergoing rapid and unprecedented changes, the ability to observe and understand how the oceans are changing on a global scale is possible through the application of environmental biomarkers. Demonstration that RNA and protein do correlate for environmentally responsive genes and the theory behind when and why these correlations occur is valuable in increasing confidence for study of metaproteomic and other meta-omic studies to the global oceans. ,− …”

Section: Results and Discussionmentioning

confidence: 99%

Why Environmental Biomarkers Work: Transcriptome–Proteome Correlations and Modeling of Multistressor Experiments in the Marine Bacterium Trichodesmium

et al. 2021

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Ocean microbial communities are important contributors to the global biogeochemical reactions that sustain life on Earth. The factors controlling these communities are being increasingly explored using metatranscriptomic and metaproteomic environmental biomarkers. Using published proteomes and transcriptomes from the abundant colony-forming cyanobacterium Trichodesmium (strain IMS101) grown under varying Fe and/ or P limitation in low and high CO 2 , we observed robust correlations of stressinduced proteins and RNAs (i.e., involved in transport and homeostasis) that yield useful information on the nutrient status under low and/or high CO 2 . Conversely, transcriptional and translational correlations of many other central metabolism pathways exhibit broad discordance. A cellular RNA and protein production/degradation model demonstrates how biomolecules with small initial inventories, such as environmentally responsive proteins, achieve large increases in fold-change units as opposed to those with a higher basal expression and inventory such as metabolic systems. Microbial cells, due to their immersion in the environment, tend to show large adaptive responses in both RNA and protein that result in transcript−protein correlations. These observations and model results demonstrate multi-omic coherence for environmental biomarkers and provide the underlying mechanism for those observations, supporting the promise for global application in detecting responses to environmental stimuli in a changing ocean.

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Section: Results and Discussionmentioning

confidence: 99%

Why Environmental Biomarkers Work: Transcriptome–Proteome Correlations and Modeling of Multistressor Experiments in the Marine Bacterium Trichodesmium

et al. 2021

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“…In addition to the standalone software, we have created web portals for METATRYP v 2 instances that use specialized databases for the marine microbial research community as well as the coronavirus research community. A private API for the marine microbial instance of METATRYP supports LCA analysis in the Ocean Protein Portal and may be further developed into a public API which can be connected to automated pipelines in the future, like GalaxyP . This major release of METATRYP features an upgraded SQL backend that supports faster speeds for database construction and data queries, enables maintenance of separate sequencing data categories within the database, and facilitates LCA analysis of shared peptides across taxa.…”

Section: Discussionmentioning

confidence: 99%

“…Additionally, we provide an overview of the METATRYP web portal for marine microorganisms and the rapid deployment of a coronavirus-specific METATRYP web portal demonstrating the application of METATRYP to various research fields. Finally, a private API was added providing LCA analysis functionality to the Ocean Protein Portal, enabling METATRYP to be inserted into other pipelines in the future.…”

Section: Introductionmentioning

confidence: 99%

METATRYP v 2.0: Metaproteomic Least Common Ancestor Analysis for Taxonomic Inference Using Specialized Sequence Assemblies—Standalone Software and Web Servers for Marine Microorganisms and Coronaviruses

et al. 2020

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We present METATRYP version 2 software that identifies shared peptides across the predicted proteomes of organisms within environmental metaproteomics studies to enable accurate taxonomic attribution of peptides during protein inference. Improvements include ingestion of complex sequence assembly data categories (metagenomic and metatranscriptomic assemblies, single cell amplified genomes, and metagenome assembled genomes), prediction of the least common ancestor (LCA) for a peptide shared across multiple organisms, increased performance through updates to the backend architecture, and development of a web portal ( ). Major expansion of the marine METATRYP database with predicted proteomes from environmental sequencing confirms a low occurrence of shared tryptic peptides among disparate marine microorganisms, implying tractability for targeted metaproteomics. METATRYP was designed to facilitate ocean metaproteomics and has been integrated into the Ocean Protein Portal ( ); however, it can be readily applied to other domains. We describe the rapid deployment of a coronavirus-specific web portal ( ) to aid in use of proteomics on coronavirus research during the ongoing pandemic. A coronavirus-focused METATRYP database identified potential SARS-CoV-2 peptide biomarkers and indicated very few shared tryptic peptides between SARS-CoV-2 and other disparate taxa analyzed, sharing <1% peptides with taxa outside of the betacoronavirus group, establishing that taxonomic specificity is achievable using tryptic peptide-based proteomic diagnostic approaches.

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“…99 of the proteins were annotated as being from Prochlorococcus and 25 were annotated as being from Synechococcus, the two genera that appeared most frequently in the GP15 protein transect. The data for all proteins are in the process of being incorporated into the Ocean Protein Portal (www.oceanproteinportal.org) (Saito et al, 2021).…”

Section: Bacterial Protein Biomarkers Along the Gp15 Surface Transectmentioning

confidence: 99%

Distributions and perturbations of the marine dissolved cobalt cycle in a changing ocean

Chmiel¹

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Cobalt is a necessary nutrient for many marine phytoplankton, but its hybrid-type nature results in small marine inventories that make it one of the scarcest bioactive trace metals in the oceans. This study examines the marine dissolved cobalt cycle in two regions: the Pacific Ocean and Antarctic coastal seas. In the North Pacific, elevated cobalt stoichiometries among phytoplankton were linked to nitrogen, iron and phosphate stress protein biomarkers at the boundaries of oceanographic provinces and upwelling zones, providing insight into the flexibility of cobalt stoichiometry. In both regions, perturbations to the marine cobalt cycle were either predicted or observed; in the equatorial Pacific, the dissolved cobalt inventory was predicted to increase by up to 28% due to the expansion of oxygen minimum zones in a warmer ocean, while in the Antarctic, melting ice shelves have the potential to shift the nutrient regime from iron limitation towards zinc and vitamin B12 limitation, resulting in higher cobalt demand and a lower dissolved cobalt inventory. When the global cobalt cycle was estimated throughout four of Earth’s systems (the lithosphere, biosphere, hydrosphere and the anthroposphere – the human environment), it was determined that the scale of the cobalt flux through the anthroposphere is only one order of magnitude lower than the inventory of the entire hydrosphere (10(9) mol Co yr-1 and 10(10) mol Co, respectively), revealing a vulnerability to anthropogenic perturbation of the marine cobalt inventory through human mining, use and disposal of cobalt if appropriate pollution abatement, disposal and recycling infrastructure is not established. In light of observed and predicted changes to cobalt biogeochemistry, this research suggests that the marine cobalt cycle is particularly vulnerable to anthropogenic perturbation from both global climate change and pollution due to its low ocean inventory and interconnection to other nutrient biogeochemical cycles.

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Development of an Ocean Protein Portal for Interactive Discovery and Education

Cited by 11 publications

References 54 publications

Why Environmental Biomarkers Work: Transcriptome–Proteome Correlations and Modeling of Multistressor Experiments in the Marine Bacterium Trichodesmium

Why Environmental Biomarkers Work: Transcriptome–Proteome Correlations and Modeling of Multistressor Experiments in the Marine Bacterium Trichodesmium

METATRYP v 2.0: Metaproteomic Least Common Ancestor Analysis for Taxonomic Inference Using Specialized Sequence Assemblies—Standalone Software and Web Servers for Marine Microorganisms and Coronaviruses

Distributions and perturbations of the marine dissolved cobalt cycle in a changing ocean

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