From the journals: December 2018

We offer a selection of recent papers on a variety of topics from the Journal of Biological Chemistry, the Journal of Lipid Research and Molecular & Cellular Proteomics.

Seeking new ways to lower cholesterol

ApoE is a key transporter of extracellular cholesterol in humans. ApoE mimetics such as Ac-hE18-NH2 have undergone clinical trials as cholesterol-lowering agents. Roger White and colleagues at the University of Alabama at Birmingham recently developed new analogs by linking different chemical groups to Ac-hE18-NH2 and investigating their ability to lower cholesterol in mice and macaques. Of the three analogs investigated, one in particular was the most effective at reducing plasma cholesterol in mice that lacked apoE and were fed a standard or high-fat diet. This analog was synthesized by linking a 12-carbon myristic acid chain to Ac-hE18-NH2. This analog also was used to treat macaques that had elevated plasma cholesterol levels. A single administration of the analog was enough to reduce cholesterol in the plasma for up to one week, depending on the dose. Cholesterol in low-density lipoproteins also was reduced significantly after treatment and did not return to baseline until one week after treatment. This work, published in the Journal of Lipid Research, may have implications for developing better cholesterol-lowering therapeutics.

Breaking up a pair of Alzheimer’s troublemakers

During Alzheimer’s disease, the protein amyloid-beta aggregates in the brain into insoluble fibrils and soluble oligomers. Amyloid-beta oligomers bind to membrane-associated prion protein. This binding leads to hallmarks of disease like over-phosphorylation of tau protein and destabilization of dendritic spines. In a paper in the Journal of Biological Chemistry, Nadine Rösener and colleagues at Heinrich-Heine-Universität Düsseldorf characterized the complex containing amyloid-beta and prion protein and showed that a D-enantiomeric peptide, identified in a previous screen of potential drug candidates, could inhibit the formation of this complex.

What determines protein complex stability?

Most of the time, individual proteins perform important functions in our systems as part of a larger complex of multiple proteins. A protein’s function is determined by certain moieties or functional groups that are attached to it after it has been synthesized from RNA. Such additions are called post-translational modifications, or PTMs. The location of such modifications within a protein determines its binding affinity with other proteins and the stability of protein–protein interactions under different conditions. A recent collaborative study by Nikolina Šoštarić and researchers in labs across three countries in Europe has identified certain PTMs that stabilize or destabilize protein complexes purified from budding yeast, or Saccharomyces cerevisiae. They focused on the evolutionarily conserved PTMs at a protein–protein interface and used various computational approaches to determine the effect of these PTMs in regulating protein-protein interactions. Their findings, published in the journal Molecular & Cellular Proteomics, suggest that acetylated lysine residues play a stabilizing role while phosphorylated residues play a destabilizing role in protein complexes. Though this study broadens our understanding of the functional role of PTMs, it remains to be seen how these findings from purified protein complexes repeat within developing cells and extrapolate to other organisms.

If you had a nickel for every UTI

E. coli and other bacteria that cause urinary tract infections sometimes carry the gene encoding the metallophore yersiniabactin, or Ybt. Ybt previously was shown to chelate iron and copper ions. In research published in the Journal of Biological Chemistry, Anne Robinson and colleagues at Washington University School of Medicine showed that Ybt additionally scavenges nickel from the extracellular environment and imports it into nickel-requiring enzymes in the bacterium. Nickel-requiring enzymes like urease have been associated with uropathogenicity, suggesting that this nickel-scavenging pathway may be important for understanding UTIs.

More than one strategy against cancer

Immunotherapy is a promising strategy against cancer, but immune responses against cancer must be quantified and controlled to avoid dangerous side effects from hyperinflammation. Christian Backes and colleagues at Saarland University wrote in the Journal of Biological Chemistry about developing a time-resolved single-cell assay for monitoring the kinetics and mechanisms of how natural killer cells cause target cell death. They found that a single NK cell could kill cancer cells via different mechanisms, either inducing apoptosis or causing membrane disruption and lysis (necrosis). Because these different types of cell death have different effects on the surrounding tumor microenvironment, this variation should be taken into account to fine-tune NK cell-based immunotherapy.

Synthetic surfactants stick around longer

Pulmonary surfactants are protein–phospholipid mixtures secreted into the alveolar space that reduce surface tension where air and liquid meet. Substitutes have been developed to treat patients who need surfactant supplementation, including preterm infants. A paper in the Journal of Lipid Research describes the differences in metabolism between synthetic and animal-derived exogenous surfactants. Anthony Postle and colleagues at the University of Southampton in the U.K. used mice to compare the metabolism of Curosurf, an animal-derived surfactant used by doctors, with that of CHF5633, a synthetic surfactant in clinical trials. Both were labeled with a carbon isotype-containing tracer and introduced to mice intranasally. The researchers extracted lipids from lung lobes harvested at various time points after introduction, and they dectected the tracer using electrospray ionization mass spectrometry. By tracking the hydrolysis products of each surfactant, Postle and colleagues were able to compare their catabolism profiles. They observed that catabolism of synthetic CHF5633 was delayed compared with that of animal-derived Curosurf, although the pathways used for metabolism were similar. They also observed enhanced recycling of the hydrolysis products of CHF5633 into new phospholipid species. Their findings have implications for how the metabolism of new synthetic pulmonary surfactants will be evaluated during clinical trials.

An alternative pathway in brain mitochondria

The mitochondrial calcium uniporter, or MCU, mediates calcium influx into mitochondria, regulating calcium-dependent processes including mitochondrial respiration. James Hamilton and colleagues at Indiana University School of Medicine showed that the role of this transporter may be different in brain-cell mitochondria than in other cell types. Whereas knocking out MCU in liver, heart and skeletal muscle mitochondria completely inhibited calcium uptake, it only slowed but did not completely inhibit uptake in mitochondria from glial cells. This suggests that another, MCU-independent calcium uptake pathway exists in brain mitochondria and may explain why ischemia-reperfusion injury has brain-specific effects. This research was published in the Journal of Biological Chemistry.

Chaos and flexibility in elastin

Elastins are the proteins that allow lungs, arteries and skin to stretch and bend. To understand these essential proteins’ mechanical properties and resilience, we need to know how the network of elastin fibers is cross-linked. In research published in the Journal of Biological Chemistry, Christoph Schräder and colleagues at Martin Luther University Halle-Wittenberg characterized these cross-links in detail in mature bovine elastin. Contrary to the previous assumption that these proteins are assembled in an orderly array, Schräder and colleagues showed that elastin formed an unordered, randomly cross-linked network.

Of dual-coding genes: database revision needed

A gene is a piece of DNA that codes for a protein. It contains a nucleotide sequence called the open reading frame, or ORF, which the RNA polymerase reads and then translates the codons (sets of three bases coding for one amino acid) into messenger RNA, which ultimately forms the protein after some post-transcriptional processing. According to the one gene–one protein hypothesis of George Beadle and Edward Tatum, each gene codes for a single protein. However, a recent paper in the journal Molecular & Cellular Proteomics by Xavier Roucou and researchers from the Université de Sherbrooke in Canada in collaboration with INSERM (Institut National de la Santé et de la Recherche Médicale) in France reiterates the existence of dual-coding genes, that is, single genes coding for different proteins from different ORFs. They showed that the gene MIEF1, known to encode 463-amino-acid protein MiD51 (an important regulator of mitochondrial division), also encodes the 70-amino-acid protein altMiD51. The smaller protein is coded by an exon originally considered noncoding. In fact, in both cell lines and tissues, the smaller protein was expressed two to six times more than the bigger protein. Although expression does not correlate with function, this study means that alternate ORFs must be incorporated in a gene’s coding sequence in the database.

Understanding oddball interferons

The 16 human type I interferons, or IFNs, regulate innate and adaptive immunity. Two of them, IFN-epsilon and IFN-kappa, have very different sequences from the others and are expressed selectively in skin, mucosa and the female reproductive system. In research published in the Journal of Biological Chemistry, Bethany Harris and colleagues at the University of Alabama report biophysical characterizations of these two IFNs’ binding interactions. They found that the two had thousandfold lower potency in signaling through the cell-surface receptor IFNAR2 than other IFNs but also had much lower affinity for an IFN-blocking viral protein. The authors speculate that these features are important for protection against viruses, including HIV, in the reproductive tract.

Stress and iron break ribosomes

Under oxidative stress, ribosomal RNA can break. The mechanism of this breakage was incompletely understood. In research published in the Journal of Biological Chemistry, Jessica Zinskie and colleagues at Rowan University showed that oxidant-induced cleavage of rRNA was site-specific and mediated by cellular iron. When free iron bound to ribosomes at specific sites, its redox activity resulted in rRNA fragmentation. The authors speculate this effect could be an adaptive mechanism for fine-tuning ribosome activity under stress.