loading page

A data-independent acquisition (DIA) assay library for quantitation of environmental effects on the kidney proteome of Oreochromis niloticus
  • +3
  • Larken Root,
  • Aurora Campo,
  • Leah MacNiven,
  • Pazit Con,
  • Avner Cnaani,
  • Dietmar Kültz
Larken Root
University of California Davis
Author Profile
Aurora Campo
Agricultural Research Organization Volcani Center
Author Profile
Leah MacNiven
University of California Davis
Author Profile
Pazit Con
Agricultural Research Organization Volcani Center
Author Profile
Avner Cnaani
Agricultural Research Organization Volcani Center
Author Profile
Dietmar Kültz
University of California Davis
Author Profile

Abstract

Interactions of organisms with their environment are complex and environmental regulation at different levels of biological organization is often non-linear. Therefore, the genotype to phenotype continuum requires study at multiple levels of organization. While studies of transcriptome regulation are now common for many species, quantitative studies of environmental effects on proteomes are needed. Here we report the generation of a data-independent acquisition (DIA) assay library that enables simultaneous targeted proteomics of thousands of Oreochromis niloticus kidney proteins using a label- and gel-free workflow that is well suited for ecologically relevant field samples. We demonstrate the usefulness of this DIA assay library by discerning environmental effects on the kidney proteome of O. niloticus. Moreover, we demonstrate that the DIA assay library approach generates data that are complimentary rather than redundant to transcriptomics data. Transcript and protein abundance differences in kidneys of tilapia acclimated to freshwater and brackish water (25 g/kg) were correlated for 2114 unique genes. A high degree of non-linearity in salinity-dependent regulation of transcriptomes and proteomes was revealed suggesting that the regulation of O. niloticus renal function by environmental salinity relies heavily on post-transcriptional mechanisms. The application of functional enrichment analyses using STRING and KEGG to DIA assay datasets is demonstrated by identifying myo-inositol metabolism, antioxidant and xenobiotic functions, and signaling mechanisms as key elements controlled by salinity in tilapia kidneys. The DIA assay library resource presented here can be adopted for other tissues and other organisms to study proteome dynamics during changing ecological contexts.

Peer review status:Published

30 Oct 2020Submitted to Molecular Ecology Resources
16 Nov 2020Submission Checks Completed
16 Nov 2020Assigned to Editor
16 Nov 2020Reviewer(s) Assigned
04 Jan 2021Review(s) Completed, Editorial Evaluation Pending
07 Apr 2021Editorial Decision: Revise Minor
30 Apr 2021Review(s) Completed, Editorial Evaluation Pending
30 Apr 20211st Revision Received
01 Jun 2021Editorial Decision: Accept
29 Jun 2021Published in Molecular Ecology Resources. 10.1111/1755-0998.13445