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Proteome targets of ubiquitin-like samp1ylation are associated with sulfur metabolism and oxidative stress in Haloferax volcanii

Journal Article · · Proteomics
 [1];  [2];  [3];  [4];  [5];  [6]
  1. Univ. of Florida, Gainesville, FL (United States). Dept. of Microbiology and Cell Science. Inst. of Food and Agricultural Sciences; Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611-0700
  2. Univ. of Florida, Gainesville, FL (United States). Dept. of Microbiology and Cell Science. Inst. of Food and Agricultural Sciences; Northwest A&F Univ., Yangling Shaanxi (China). College of Forestry
  3. Univ. of Florida, Gainesville, FL (United States). Dept. of Microbiology and Cell Science. Inst. of Food and Agricultural Sciences
  4. Northwest A&F Univ., Yangling Shaanxi (China). College of Forestry
  5. Univ. of Florida, Gainesville, FL (United States). Proteomics and Mass Spectrometry. Interdisciplinary Center for Biotechnology Research. Dept. of Biology. Genetics Inst.
  6. Univ. of Florida, Gainesville, FL (United States). Dept. of Microbiology and Cell Science. Inst. of Food and Agricultural Sciences. Genetics Inst.
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Small archeal modifier proteins (SAMPs) are related to ubiquitin in tertiary structure and in their isopeptide linkage to substrate proteins. SAMPs also function in sulfur mobilization to form biomolecules such as molybdopterin and thiolated tRNA. While SAMP1 is essential for anaerobic growth and covalently attached to lysine residues of its molybdopterin synthase partner MoaE (K240 and K247), the full diversity of proteins modified by samp1ylation is not known. In this paper, we expand the knowledge of proteins isopeptide linked to SAMP1. LC-MS/MS analysis of -Gly-Gly signatures derived from SAMP1 S85R conjugates cleaved with trypsin was used to detect sites of sampylation (23 lysine residues) that mapped to 11 target proteins. Many of the identified target proteins were associated with sulfur metabolism and oxidative stress including MoaE, SAMP-activating E1 enzyme (UbaA), methionine sulfoxide reductase homologs (MsrA and MsrB), and the Fe-S assembly protein SufB. Several proteins were found to have multiple sites of samp1ylation, and the isopeptide linkage at SAMP3 lysines (K18, K55, and K62) revealed hetero-SAMP chain topologies. Follow-up affinity purification of selected protein targets (UbaA and MoaE) confirmed the LC-MS/MS results. 3D homology modeling suggested sampy1ylation is autoregulatory in inhibiting the activity of its protein partners (UbaA and MoaE), while occurring on the surface of some protein targets, such as SufB and MsrA/B. Finally and overall, we provide evidence that SAMP1 is a ubiquitin-like protein modifier that is relatively specific in tagging its protein partners as well as proteins associated with oxidative stress response.
Research Organization:
Northwest A&F Univ., Yangling Shaanxi (China); Univ. of Florida, Gainesville, FL (United States)
Sponsoring Organization:
China Scholarship Council; National Inst. of Health (NIH) (United States); USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
Grant/Contract Number:
FG02-05ER15650
OSTI ID:
1467086
Journal Information:
Proteomics, Journal Name: Proteomics Journal Issue: 7 Vol. 16; ISSN 1615-9853
Publisher:
WileyCopyright Statement
Country of Publication:
United States
Language:
English

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Cited By (7)

Methionine Sulfoxide Reductases of Archaea journal September 2018
Modifying Post‐Translational Modifications: A Strategy Used by Archaea for Adapting to Changing Environments?: Manipulating the Extent, Position, or Content of Post‐Translational Modifications May Help Archaea Adapt to Environmental Change journal March 2020
Rpn11-mediated ubiquitin processing in an ancestral archaeal ubiquitination system journal July 2018
Mechanistic insight into protein modification and sulfur mobilization activities of noncanonical E1 and associated ubiquitin-like proteins of Archaea journal October 2016
The secreted salivary proteome of Asian citrus psyllid Diaphorina citri: Saliva proteins of D. citri journal September 2018
Methionine Sulfoxide Reductase A (MsrA) and Its Function in Ubiquitin-Like Protein Modification in Archaea journal September 2017
Several One-Domain Zinc Finger µ-Proteins of Haloferax Volcanii Are Important for Stress Adaptation, Biofilm Formation, and Swarming journal May 2019

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59 BASIC BIOLOGICAL SCIENCES
archaea
microbiology
oxidative stress
sampylation
sulfur mobilization
ubiquitin