Chemical isotope labeling for quantitative proteomics

X Tian, HP Permentier, R Bischoff - Mass spectrometry reviews, 2023 - Wiley Online Library
Advancements in liquid chromatography and mass spectrometry over the last decades have
led to a significant development in mass spectrometry‐based proteome quantification …

Complex regulation in a Comamonas platform for diverse aromatic carbon metabolism

RA Wilkes, J Waldbauer, A Carroll… - Nature Chemical …, 2023 - nature.com
Critical to a sustainable energy future are microbial platforms that can process aromatic
carbons from the largely untapped reservoir of lignin and plastic feedstocks. Comamonas …

Mechanisms of Polyethylene Terephthalate Pellet Fragmentation into Nanoplastics and Assimilable Carbons by Wastewater Comamonas

RA Wilkes, N Zhou, AL Carroll, O Aryal… - Environmental …, 2024 - ACS Publications
Comamonadaceae bacteria are enriched on poly (ethylene terephthalate)(PET)
microplastics in wastewaters and urban rivers, but the PET-degrading mechanisms remain …

Oncoproteomics: Current status and future opportunities

Y He, A Mohamedali, C Huang, MS Baker, EC Nice - Clinica Chimica Acta, 2019 - Elsevier
Oncoproteomics is the systematic study of cancer samples using omics technologies to
detect changes implicated in tumorigenesis. Recent progress in oncoproteomics is already …

Analogous metabolic decoupling in Pseudomonas putida and Comamonas testosteroni implies energetic bypass to facilitate gluconeogenic growth

RA Wilkes, J Waldbauer, L Aristilde - MBio, 2021 - Am Soc Microbiol
Gluconeogenic carbon metabolism is not well understood, especially within the context of
flux partitioning between energy generation and biomass production, despite the importance …

Tracking nitrogen allocation to proteome biosynthesis in a marine microbial community

AE Zimmerman, JC Podowski, GE Gallagher… - Nature …, 2023 - nature.com
Microbial growth in many environments is limited by nitrogen availability, yet there is limited
understanding of how complex communities compete for and allocate this resource. Here …

Carbon substrate re‐orders relative growth of a bacterium using Mo‐, V‐, or Fe‐nitrogenase for nitrogen fixation

KE Luxem, AML Kraepiel, L Zhang… - Environmental …, 2020 - Wiley Online Library
Biological nitrogen fixation is catalyzed by the molybdenum (Mo), vanadium (V) and iron
(Fe)‐only nitrogenase metalloenzymes. Studies with purified enzymes have found that the …

Membrane lipid and expression responses of Saccharolobus islandicus REY15A to acid and cold stress

BK Chiu, J Waldbauer, FJ Elling, ÖZ Mete… - Frontiers in …, 2023 - frontiersin.org
Archaea adjust the number of cyclopentane rings in their glycerol dibiphytanyl glycerol
tetraether (GDGT) membrane lipids as a homeostatic response to environmental stressors …

Disproportionate Carbon Dioxide Efflux in Bacterial Metabolic Pathways for Different Organic Substrates Leads to Variable Contribution to Carbon-Use Efficiency

CM Mendonca, L Zhang, JR Waldbauer… - … Science & Technology, 2024 - ACS Publications
Microbial organic matter turnover is an important contributor to the terrestrial carbon dioxide
(CO2) budget. Partitioning of organic carbons into biomass relative to CO2 efflux, termed …

DsrC is involved in fermentative growth and interacts directly with the FlxABCD–HdrABC complex in Desulfovibrio vulgaris Hildenborough

D Ferreira, SS Venceslau, R Bernardino… - Environmental …, 2023 - Wiley Online Library
DsrC is a key protein in dissimilatory sulfur metabolism, where it works as co‐substrate of
the dissimilatory sulfite reductase DsrAB. DsrC has two conserved cysteines in a C‐terminal …