Shrub expansion in the Arctic may induce large-scale carbon losses due to changes in plant-soil interactions

Background Tall deciduous shrubs are increasing in range, size and cover across much of the Arctic, a process commonly assumed to increase carbon (C) storage. Major advances in remote sensing have increased our ability to monitor changes aboveground, improving quantification and understanding of arctic greening. However, the vast majority of C in the Arctic is stored in soils, where changes are more uncertain. Scope We present pilot data to argue that shrub expansion will cause changes in rhizosphere processes, including the development of new mycorrhizal associations that have the potential to promote soil C losses that substantially exceed C gains in plant biomass. However, current observations are limited in their spatial extent, and mechanistic understanding is still developing. Extending measurements across different regions and tundra types would greatly increase our ability to predict the biogeochemical consequences of arctic vegetation change, and we present a simple method that would allow such data to be collected. Conclusions Shrub expansion in the Arctic could promote substantial soil C losses that are unlikely to be offset by increases in plant biomass. However, confidence in this prediction is limited by a lack of information on how soil C stocks vary between contrasting Arctic vegetation communities; this needs to be addressed urgently

Uncovering protein–protein interactions through a team-based undergraduate biochemistry course

How can we provide fertile ground for students to simultaneously explore a breadth of foundational knowledge, develop cross-disciplinary problem-solving skills, gain resiliency, and learn to work as a member of a team? One way is to integrate original research in the context of an undergraduate biochemistry course. In this Community Page, we discuss the development and execution of an interdisciplinary and cross-departmental undergraduate biochemistry laboratory course. We present a template for how a similar course can be replicated at other institutions and provide pedagogical and research results from a sample module in which we challenged our students to study the binding interface between 2 important biosynthetic proteins. Finally, we address the community and invite others to join us in making a larger impact on undergraduate education and the field of biochemistry by coordinating efforts to integrate research and teaching across campuses

In a semester of Biochemistry Superlab, students investigated the protein–protein interactions involved in the β-hydroxylation of the natural product skyllamycin.

<p>The skyllamycin peptide is constructed by <i>Streptomyces</i> bacteria via a NRPS involving 11 biosynthetic modules (“M”), composed of catalytic domains such as the A, PCP, and C domains. The <i>in trans</i> cytochrome P450 (P450_sky, orange) interacts with PCP-bound amino acids on modules 5, 7, and 11 to install β-hydroxyl groups (highlighted in orange on the structure of skyllamycin, right). As a class, we tackled the central question: What is the biochemical basis for the selectivity of the interaction of PCP from module 7 with P450_sky to install the hydroxyl group on the L-(OMe)-Tyr (incorporated at the boxed position of skyllamycin)? A, adenylation; C, condensation; NRPS, non-ribosomal peptide synthetase; PCP, peptidyl carrier protein.</p

SV-AUC data collected and analyzed by students to obtain dissociation constants for P450_sky and mutants of P450_sky interacting with inhibitor-bound PCP7_sky (L-imidazoyl-PCP7_sky).

<p>Comparisons of the <i>c(s)</i> distributions are shown for 10 μM P450_sky wild type alone and in complex with 60 μM L-imidazoyl-PCP7_sky L62A, L-imidazoyl-PCP7_sky F66A, and L-imidazoyl-PCP7_sky wild type. A) 280 nm (protein), B) 418 nm (heme). In general, shifts to the right suggest that the reaction boundary favors tighter binding. SV-AUC, sedimentation velocity experiments with an analytical ultracentrifuge.</p

General workflow for students investigating the noncovalent interactions involved in P450_sky-catalyzed β-hydroxylation of L-(OMe)-Tyr.

<p>This involves computational analysis (Step 1), molecular biology or synthetic chemistry (Step 2), protein purification (Step 3), chemoenzymatic assays (Step 4), and biochemical and biophysical experiments (Step 5). This workflow is a template for realizing an integrated science curriculum, as described and assessed by the Interdisciplinary Learning Consortium [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003145#pbio.2003145.ref009" target="_blank">9</a>]. PCP, peptidyl carrier protein.</p

Structures of the skyllamycin NRPS PCP domain (PCP7_sky, green) bound to a hydroxylating cytochrome P450 (P450_sky, multicolored).

<p>Students visualized this structure in PyMOL (A) and evaluated the roles of 4 amino acid residues at the P450_sky–PCP7_sky interface (B). See <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2003145#pbio.2003145.box002" target="_blank">Box 2</a> for details. NRPS, non-ribosomal peptide synthetase; PCP, peptidyl carrier protein.</p