From the journals

Published September 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.

Why the immune system needs a breath of fresh air

In lung disorders such as chronic obstructive pulmonary disease, elevated carbon dioxide in the blood (hypercapnia) is associated with suppressed immune function. A paper in the Journal of Biological Chemistry describes how the connection between hypercapnia and immunosuppression is mediated by the NF-kappaB signaling pathway. Eoin P. Cummins and colleagues investigated the basis of the CO2-sensitivity of NF-kappaB signaling and found that “noncanonical” transcription factors RelB and p100 were translocated to the nucleus in response to CO2. They also identified a mechanism of CO2-dependent cleavage of RelB.

Enzymatic surprises from cow stomach fungi

Because the microbial communities in the rumens of cows and other large herbivores efficiently process large amounts of plant matter, they are a potential source of new enzymes that can be used in biofuels and other applications. In a paper in the Journal of Biological Chemistry, D. Wade Abbott and colleagues describe how they investigated family 39 glycoside hydrolases from rumen fungi and found that these hydrolases release rare arabinosyl-containing glycans from plant hemicelluloses and pectins, revealing new functional diversity in this enzyme family.

Protein sequences from metazoan Ctr1 and Ctr2 were aligned and analyzed for conservation with the ConSurf server using a Bayesian evolution method. Shown are the human Ctr1 and Ctr2 proteins with amino acids that represent variable (blue), neutral (white), or conserved (red) positions. Arrows point to the highly conserved MXXXM motif necessary for copper transport. Asterisks denote residues Phe-77 and Glu-91 in human Ctr1 as well as Leu-34 and Lys-47 in human Ctr2.

A tale of two copper transporters

Copper is an essential cofactor for enzymes involved in many different biological processes. The mammalian copper transporter Ctr1 plays essential roles in embryonic development, whereas the homologous protein Ctr2 lacks transporter activity but regulates Ctr1. In a paper in the Journal of Biological Chemistry, Dennis J. Thiele and colleagues describe their finding that Ctr1 and Ctr2 arose as a result of an ancient gene duplication and that copper-dependent cell growth in Ctr1-lacking cells could be rescued by mutations in Ctr2 generated via random mutagenesis that restored its copper transporter activity.

How calmodulin captures K-Ras in cancer

The calcium-binding protein calmodulin promotes cell proliferation in some cancers by selectively binding to the oncoprotein K-Ras and extracting it from cell membranes, leading to the creation of an oncogenic signaling complex. In a paper in the Journal of Biological Chemistry, Ruth Nussinov and colleagues describe how they carried out molecular dynamics simulations that suggested that the hypervariable region of K-Ras4B wraps around calmodulin’s flexible linker region in a stable but highly dynamic interaction necessary for K-Ras release.

Omega-3s make sperm flexible and viable

DHA is an essential omega-3 fatty acid that increases the flexibility of cell membranes. Takao Shimizu and colleagues write in the Journal of Biological Chemistry about how they discovered that knocking out an enzyme required for incorporation of DHA-containing phospholipids into cell membranes leads to male infertility in mice. Observations of spermatogenesis in these mice suggested that DHA-induced membrane flexibility is necessary for sperm maturation. In a companion paper, Shimizu and colleagues examined DHA’s role in the retina.

Dissecting reactions in miniature membranes

Hydrogen sulfide is a signaling molecule that is toxic at high concentrations. The first step of detoxification of H2S in mitochondria is catalyzed by sulfide quinoneoxidoreductase, or SQR. In a paper in the Journal of Biological Chemistry, Ruma Banerjee and colleagues describe how they analyzed the kinetics of this reaction using SQR embedded in nanodiscs (synthetic soluble membranes) rather than solubilized in detergent, simulating an environment more similar to the enzyme’s natural membrane-embedded state. Using this approach, they identified the rate-limiting step and sulfane sulfur acceptor in this reaction.

Knocking out DOCK2 revs mouse weight loss

There’s still much to be learned about the connections between inflammation and obesity. In a recent paper in the Journal of Lipid Research, researchers created mice deficient in the protein DOCK2 to see what effects the deficiency might have on weight gain and metabolism. DOCK2 is short for dedicator of cytokinesis 2. It ordinarily is expressed in white blood cells. Compared with normal mice, the mice deficient in DOCK2 gained less weight and had more active metabolisms when they ate a high-fat chow. They also had less adipose tissue and lower inflammation than wild-type mice. DOCK2, it seems, might end up a target worthy of pursuit in the search for therapies for obesity. The work was overseen by Shi-You Chen at the University of Georgia.

Method helps visualize lipid-based PTMs

Lipidation is the covalent binding of a lipid group to a peptide chain. It’s one form of post-translational modification that contributes to the diversity of the proteome. In a paper in the Journal of Lipid Research, a team of researchers led by Tamara L. Kinzer–Ursem and Sarah Calve at Purdue University report the development of a new method of imaging proteins, both in vitro and in vivo, that have been modified by the addition of myristic acid at the N-terminus. The researchers report that the distribution of these proteins varies dramatically between undifferentiated and differentiated muscle cells in zebrafish. Their study indicates that this fluorescent detection method can help those studying the roles that myristoylation and other lipid modifications play in disease.

Bacterial cellulose preserves native cellular phenotype

Conventional culture of primary cells on rigid and hydrophobic plastic surfaces may cause phenotypic alterations, contributing to the discrepancy between in vivo and in vitro biological models. In a paper in Molecular & Cellular Proteomics, Gerhard Feil and colleagues describe how they developed a bacterial cellulose cell culture support called Xellulin, which they showed to preserve important features of the native phenotype of primary cells. Transcriptomic and proteomic analyses revealed that the gene expression of cells propagated on Xellulin resembled native cells significantly more than cells grown on plastic, demonstrating the potential of Xellulin as a tool to promote an in vivo-like phenotype in cell culture.

Desorption electrospray ionization (DESI) is an ambient ionization mass spectrometric imaging technique. Electrospray droplets are formed when high voltage is applied to the solvent. Desorbed analyte is vacuumed into the mass spectrometer inlet, separated by m/z, and detected. After the sample is slowly rastered beneath the DESI source and mass spectrometer inlet, an image of the sample surface can be re-created from the mass spectral data.

Imaging lipid metabolism in the mouse brain

At any given moment, myriad reactions occur in a cell and, on a larger scale, in a tissue. Each reaction type has its own requirements, and so the cell has specialized compartments to establish those conditions. A new paper in the Journal of Lipid Research describes the use of DESI-MS (short for desorption electrospray ionization mass spectrometry) to measure lipid metabolism in different parts of mouse brain. The researchers, led by John C. Price at Brigham Young University, showed that lipid turnover rates vary from region to region. They note that their study is the first to image metabolism of specific lipids (they picked four for this work) but that their techniques could be applied to any identifiable molecule.

Understanding a new tuberculosis vaccine

Mycobacterium vaccae has been shown to be a promising vaccine against tuberculosis; however, the mechanisms by which it exerts immunomodulatory effects in humans are not fully understood. In a paper in Molecular & Cellular Proteomics, Jianhua Zheng and colleagues describe how they performed a proteogenomic analysis of M. vaccae in which they identified the expression of 3,387 proteins, including 581 hypothetical proteins and 38 novel proteins that previously were unannotated. Further investigation revealed 35 candidate antigen proteins, a few of which show highly immunogenic activity, providing insights into the physiology and mechanisms of M. vaccae immunotherapy.

Protein dynamics in brain development

Resolving protein expression patterns throughout tissue development in specific anatomical regions remains technologically challenging. Ugljesa Djuric and colleagues tackled this issue in understanding neurodevelopment by profiling proteins isolated from formalin-fixed, paraffin-embedded cerebral regions at different fetal developmental stages using mass spectrometry. In a paper in Molecular & Cellular Proteomics, they describe how they found dynamic changes in protein abundance throughout brain development and identified a number of novel region-specific protein expression patterns. This spatiotemporal proteomic profiling strategy offers the potential for understanding development of other tissues and pathogenesis of diseases.

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.