Selenocysteine: Wherefore Art Thou?

Quantitative Proteomics Reveals UGA-Independent Misincorporation of Selenocysteine throughout the Escherichia coli Proteome

Selenocysteine is cotranslationally inserted into polypeptide chains by recoding the stop codon UGA. However, selenocysteine has also been found to be misincorporated into a small number of proteins displacing cysteines in previous studies, but such misincorporation has not yet been examined at the proteome level thoroughly. We performed label-free quantitative proteomics analysis on Escherichia coli grown in a high-selenium medium to obtain a fuller picture of selenocysteine misincorporation in its proteome. We found 139 misincorporation sites, including 54 recurred in all biological replicates, suggesting that some cysteine sites are more prone to be misincorporated than others. However, sequence and evolutionary conservation analysis showed no clear pattern among these misincorporation sites. We hypothesize that misincorporations occur randomly throughout the proteome, but the degradation rate of such misincorporated proteins varies depending on the impact of the misincorporation on protein function and stability, leading to the differential detectability of misincorporated sites by proteomics. Our hypothesis is further supported by two observations: (1) cells cultured with severely limited sulfur still retained a substantial proportion of normal cysteine counterparts of all of the found misincorporated proteins and (2) proteins involved in protein folding and proteolysis were highly upregulated in high-selenium culture.

Facultative protein selenation regulates redox sensitivity, adipose tissue thermogenesis, and obesity

Oxidation of cysteine thiols by physiological reactive oxygen species (ROS) initiates thermogenesis in brown and beige adipose tissues. Cellular selenocysteines, where sulfur is replaced with selenium, exhibit enhanced reactivity with ROS. Despite their critical roles in physiology, methods for broad and direct detection of proteogenic selenocysteines are limited. Here we developed a mass spectrometric method to interrogate incorporation of selenium into proteins. Unexpectedly, this approach revealed facultative incorporation of selenium as selenocysteine or selenomethionine into proteins that lack canonical encoding for selenocysteine. Selenium was selectively incorporated into regulatory sites on key metabolic proteins, including as selenocysteine-replacing cysteine at position 253 in uncoupling protein 1 (UCP1). This facultative utilization of selenium was initiated by increasing cellular levels of organic, but not inorganic, forms of selenium. Remarkably, dietary selenium supplementation elevated facultative incorporation into UCP1, elevated energy expenditure through thermogenic adipose tissue, and protected against obesity. Together, these findings reveal the existence of facultative protein selenation, which correlates with impacts on thermogenic adipocyte function and presumably other biological processes as well.

Selenium-Encoded Isotopic Signature Targeted Profiling

Selenium (Se), as an essential trace element, plays crucial roles in many organisms including humans. The biological functions of selenium are mainly mediated by selenoproteins, a unique class of selenium-containing proteins in which selenium is inserted in the form of selenocysteine. Due to their low abundance and uneven tissue distribution, detection of selenoproteins within proteomes is very challenging, and therefore functional studies of these proteins are limited. In this study, we developed a computational method, named as selenium-encoded isotopic signature targeted profiling (SESTAR), which utilizes the distinct natural isotopic distribution of selenium to assist detection of trace selenium-containing signals from shotgun-proteomic data. SESTAR can detect femtomole quantities of synthetic selenopeptides in a benchmark test and dramatically improved detection of native selenoproteins from tissue proteomes in a targeted profiling mode. By applying SESTAR to screen publicly available datasets from Human Proteome Map, we provide a comprehensive picture of selenoprotein distributions in human primary hematopoietic cells and tissues. We further demonstrated that SESTAR can aid chemical-proteomic strategies to identify additional selenoprotein targets of RSL3, a canonical inducer of cell ferroptosis. We believe SESTAR not only serves as a powerful tool for global profiling of native selenoproteomes, but can also work seamlessly with chemical-proteomic profiling strategies to enhance identification of target proteins, post-translational modifications, or protein-protein interactions.

Selenium Levels in Serum, Red Blood Cells, and Cerebrospinal Fluid of Alzheimer's Disease Patients: A Report from the Australian Imaging, Biomarker & Lifestyle Flagship Study of Ageing (AIBL)

Selenium (Se) protects cells against oxidative stress damage through a range of bioactive selenoproteins. Increased oxidative stress is a prominent feature of Alzheimer's disease (AD), and previous studies have shown that Se deficiency is associated with age-related cognitive decline. In this study, we assessed Se status in different biofluids from a subgroup of participants in the Australian Imaging, Biomarkers and Lifestyle Flagship Study of Ageing. As Se in humans can either be an active component of selenoproteins or inactive via non-specific incorporation into other proteins, we used both size exclusion chromatography-inductively coupled plasma-mass spectrometry (SEC-ICP-MS) and tandem mass spectrometry to characterize selenoproteins in serum. We observed no differences in total Se concentration in serum or cerebrospinal fluid of AD subjects compared to mildly cognitively impairment patients and healthy controls. However, Se levels in erythrocytes were decreased in AD compared to controls. SEC-ICP-MS analysis revealed a dominant Se-containing fraction. This fraction was subjected to standard protein purification and a bottom-up proteomics approach to confirm that the abundant Se in the fraction was due, in part, to selenoprotein P. The lack of change in the Se level is at odds with our previous observations in a Brazilian population deficient in Se, and we attribute this to the Australian cohort being Se-replete.