From the journals

Published October 01 2017

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.

G-protein signaling in light of light

Signals from light to the visual system activate rhodopsin, a G-protein-coupled receptor that catalyzes the dissociation of the G protein transducin. Using several new biochemical strategies, Yang Gao and colleagues isolated and characterized a fully functional and stable complex of light-activated rhodopsin and transducin. Their model, published in the Journal of Biological Chemistry, resolved the stoichiometry of the interaction and showed that the flexible helical domain of the G protein can adopt a range of open positions. Characterizing this complex enables further mechanistic studies of visual signal transduction.

Short peptides make rats eat more

Neuropeptides are short chains of amino acids that regulate a wide range of neurological processes, including food intake and body weight. Identifying which neuropeptides and how they change in response to feeding would offer a potential avenue for the treatment of eating disorders. In a paper in Molecular & Cellular Proteomics, Lingjun Li and colleagues describe how they employed a quantitative proteomics strategy to identify these neuropeptides in the brains of rats that were fed or deprived of food. They further demonstrated that when a few of the identified neuropeptides were injected directly into the brain, the rats would increase significantly their food and water intake.

Lipids go spelunking

Caveolae, or “little caves,” are specialized nanodomains enriched in cholesterol and sphingolipids that form in plasma membranes and participate in signaling, trafficking and metabolic processes. Takashi Hirama and colleagues investigated the fine-scale interactions between specific types of lipids and caveola-specific proteins. Using live-cell single-particle tracking, they showed that the phospholipid phosphatidylserine was required for caveola assembly and stability. The results were published in the Journal of Biological Chemistry.

The genes involved in tumorigenesis show tissue-specific expression in Xenopus embryos. (A) Whole-mount in situ hybridization, or WMISH, detection of expression of genes coding for chromatin modification enzymes. (B) WMISH detection of expression of EMT marker genes. Expression of xk81a1 and sox2 is shown as control. Mid to late neurula and tailbud embryos were used. Abbreviations: A, anterior; ba, branchial arch; df, dorsal fin; ep, epidermis; ev, ear vesicle; ey, eye; fb, forebrain; hb, hindbrain; he, heart; mb, midbrain; nc, neural crest; np, neural plate; nt, neural tube; P, posterior; pcv, posterior cardinal vein; pl, plexus; pn, pronephros; sc, spinal cord; tb, tail bud.Nanjing university

What cancer can teach us about embryonic neural development

Cancer cells can be viewed as improperly differentiated immature cells. In a paper published in the Journal of Biological Chemistry, Ying Cao and colleagues present a series of observations that suggest cancer cells are similar to embryonic neural cells. Xenopus embryos expressed pan-cancer-promoting genes and pathways primarily during neurulation, whereas tumor suppressor genes largely were expressed in non-neural cells. Inhibition of cancer-related enzymes involved in epigenetic modifications resulted in neurallike differentiation of cancer cells. Together these results suggest some common regulatory networks underlying tumorigenesis and neural development.

Gut check: give cholesterol credit

Owing to its role in cardiovascular disease, cholesterol has a bad reputation. But cholesterol is necessary for cellular-membrane integrity and other functions that life requires. We can add to cholesterol’s list of positives, according to new research in the Journal of Lipid Research, its role in shoring up the intestine. SREBP-2 is a transcription factor that regulates cholesterol biosynthesis. Researchers led by Luke J. Engelking engineered mice that lack SREBP-2 in the intestine, making them deficient in cholesterol there. Engelking’s team reported that the mice required exogenous cholesterol to maintain intestinal integrity and, ultimately, survive. Furthermore, as David Y. Hui of the University of Cincinnati College of Medicine emphasized in a commentary accompanying the paper, the work documents that “cholesterol itself, but not intermediates in the SREBP-2-regulated cholesterol biosynthetic pathway, is required” for survival of the intestinal mucosa.

Short genes, high cholesterol?

Adults who are short are known to be at greater risk of heart disease than their average and tall peers. A team of researchers led by Lee A. Pyles reports in the Journal of Lipid Research that, as it is with adults, short stature in children is associated with higher levels of low-density lipoprotein (commonly known as bad cholesterol). The finding, which resulted from a study of more than 63,000 West Virginia schoolchildren, supports “the observations that factors in addition to diet, physical activity and (body mass index) determine serum cholesterol,” the authors wrote. They suggest that it may be wise to factor in children’s heights, in addition to family history, when considering childhood screening for hyperlipidemia.

Undeterred by damaged DNA

If the DNA replication machinery of a cell encounters a damaged portion of DNA, or DNA lesion, it either skips it or waits for the recruitment of a specialized DNA polymerase capable of synthesis across the lesion. In a paper published in the Journal of Biological Chemistry, Philip Nevin and colleagues found that the E. coli DNA polymerase III — within its replisome complex but not by itself — could bypass certain types of lesions without the need for specialized trans-lesion polymerases. This mechanism reveals additional diversity in DNA damage responses.

Discovery of a novel methyltransferase

Protein methylation is emerging as a widespread and important post-translational modification that regulates diverse cellular processes, but little is known about the enzymes that catalyze this reaction. In a paper in Molecular & Cellular Proteomics, Marc Wilkins and colleagues used the CRISPR/Cas9 system to knock out a putative methyltransferase, METTL21B and, using targeted mass spectrometry, showed that it methylates the elongation factor eEF1A. Proteomic analysis of METTL21B knockout cells revealed changes in biological processes and complexes related to eEF1A function, prompting the authors to suggest that METTL21B be renamed eEF1A-KMT3.

Prion disease — the lipid connection

There are no effective therapies to eliminate or even slow the progression of transmissible spongiform encephalopathies, such as Creutzfeldt–Jakob disease, mad cow disease and scrapie, all of which are fatal. Given that previous studies have found that lipids affect the replication and propagation of the pathogenic proteins that cause the devastating neurodegeneration seen in TSEs, a team of researchers decided to investigate how very low levels of circulating plasma lipids would affect mice infected with scrapie. The project, led by Catherine Desrumaux and Véronique Perrier, used an established mouse model deficient in the phospholipid transfer protein. Mice deficient in PLTP have significantly lower plasma cholesterol than normal. The researchers infected the knockout mice with a scrapie strain and found that the mice lived longer than wild-type mice that also had been infected. In addition, when the knockout mice were fed a high-fat diet, which raised their lipid levels, they developed more prion deposits in the brain and died sooner. In their paper in the Journal of Lipid Research, the researchers say the results suggest that lowering plasma cholesterol levels may benefit patients with prion disease.

Reprogramming cells from type 1 diabetes patients

Type 1 diabetes, in which patients do not produce enough insulin from their pancreatic beta cells, potentially could be treated by transplanting healthy pancreatic tissues into patients. In a paper published in the Journal of Biological Chemistry, Gohar S. Manzar and colleagues generated glucose-responsive insulin-producing beta cells from induced pluripotent stem cells derived from type I diabetes patients. Key to the differentiation of insulin-producing cells was a treatment that caused transient demethylation in the stem cells. When injected, these cells reduced hyperglycemia in mice.

Restoring cholesterol homeostasis

Niemann-Pick type C is a rare neurodegenerative disorder characterized by the abnormal accumulation of cholesterol and other lipids in the late endosomes and lysosomes. A histone deacetylase inhibitor, Vorinostat, has been shown to restore cholesterol homeostasis in cells derived from NPC patients; however, the mechanisms by which it does this are not known. In a paper in Molecular & Cellular Proteomics, William Balch and colleagues performed a comparative proteomic profiling on these cells, where they found that Vorinostat modulates the expression of lysosomal proteins, especially lysosomal acid lipase, which contributes to cholesterol efflux from the cell.

A biophysical celebration of a DNA-binding protein

Single-stranded DNA–binding protein, or SSB, is essential during DNA replication and repair. Unlike E. coli SSB, human mitochondrial SSB lacks a disordered C-terminal domain. In a Journal of Biological Chemistry paper, Yufeng Qian and Kenneth A. Johnson characterized the kinetics and energetics of the binding between single-stranded DNA and mitochondrial SSB using an array of quantitative approaches, including DNA footprinting, fluorescence anisotropy, isothermal titration calorimetry and stopped-flow experiments integrated with real-time statistical evaluation.

The function of a tuberculosis prodrug activator

Drug-resistant tuberculosis is a public health threat. Thyenopyrimidine compounds such as TP053 are promising anti-tuberculosis drugs because they kill both replicating and nonreplicating bacteria. TP053 is a prodrug that must be activated by a Mycobacterium tuberculosis enzyme whose function was previously unknown. In research published in the Journal of Biological Chemistry, Joris Messens and colleagues characterized this enzyme and found that it is a mycoredoxin involved in the pathogen’s oxidative stress response.

The connection between hepatitis C and diabetes

People infected with hepatitis C virus, or HCV, commonly develop type II diabetes. Hervé Lerat and colleagues used transgenic mice expressing HCV proteins in the liver to examine the pathways leading to this state, finding that expression of HCV proteins resulted in impaired insulin signaling via uncoupling of the Akt/FOXO1 pathway, leading to insulin resistance. The results were published in the Journal of Biological Chemistry.

Sasha Mushegian Sasha Mushegian is scientific communicator for JBC.

Angela Hopp Angela Hopp is executive editor of ASBMB Today and communications director for the ASBMB.

Saddiq Zahari Saddiq Zahari is a postdoctoral scholar at the University of California, San Francisco, and the editor for manuscript integrity at MCP.