Multi-Omic Profiling of Rare Earth Element Metabolism in the Extremophilic Methylotroph Methylotuvimicrobium Alcaliphilum 20ZR

William Gebbie

Program: Master’s Program in Bioinformatics & Medical Informatics
Date: Thursday, February 29, 2024
Time: 2:00 PM

Abstract

Rare Earth Elements (REEs) are vital for clean renewable energy production and storage; however, mineral-mining comes with a high environmental cost. Novel nature-inspired pathways for REE recovery are thus urgently needed. REEs have been shown to be involved in the primary methylotrophic metabolic pathways as cofactors in various enzymes. The biological pathways for REE uptake and sequestration are becoming a reservoir of innovations for advancing new-mining strategies. In this thesis, I take a bioinformatic approach to identify proteins contributing to REE metabolism in Methylotuvimicrobium alcaliphilum 20ZR, a model extremophilic methanotrophic bacteria.

My research starts with collection and re-analysis of transcriptomics, proteomics, and regulatory datasets previously generated. M. alcaliphilum 20ZR -omics data analyzed in this thesis includes: (1) RNA-seq data from 17 different samples representing transcripts from REE supplemented, calcium (Ca) supplemented, and no Ca or REE supplemented growth conditions, (2) mass spectrometry spectral-count data representing protein abundances from 12 samples from lanthanum (La) supplemented and Ca supplemented growth conditions at different timepoints in growth, (3) 2 sets of genes upregulated in REE supplemented conditions identified through previous regulatory studies, and (4) a protein orthology table of for 122 methylotrophic organisms. The bioinformatics pipeline developed uses differential expression analysis at both the transcripts and protein level to identify initial sets of proteins upregulated in the presence of REEs and subsequently filters and characterizes them for a resulting final set of proteins predicted to be involved in REE binding and/or metabolism.

Using the newly developed pipeline for data integration, 31 proteins involved in the putative binding and/or metabolism of REEs were identified which included proteins predicted to contribute to hemin transport, heme iron utilization, toxin secretion, ABC transportation, and iron-sulfur cluster assembly. A subset of these proteins includes exported proteins of unknown function. The proteins identified from this work will contribute to the general knowledge of REE metabolism in M. alcaliphilum 20ZR, other methylotrophs, and possibly non-methylotrophic organisms which possess orthologous counterparts within their genomes. These proteins also represent new targets for downstream metabolic engineering endeavors for the sequestration of REEs from mining tailings.