Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

Identification of the coding elements in the genome is a fundamental step to understanding the building blocks of living systems. Short peptides (< 100 aa) have emerged as important regulators of development and physiology, but their identification has been limited by their size. We have leveraged the periodicity of ribosome movement on the mRNA to define actively translated ORFs by ribosome footprinting. This approach identifies several hundred translated small ORFs in zebrafish and human. Computational prediction of small ORFs from codon conservation patterns corroborates and extends these findings and identifies conserved sequences in zebrafish and human, suggesting functional peptide products (micropeptides). These results identify micropeptide‐encoding genes in vertebrates, providing an entry point to define their function in vivo.     

Increasing relevance of spring temperatures for Norway spruce trees in Davos,Switzerland, after the 1950s

Key message

Relevance of spring temperatures for tree-ring growth steadily increased since 1950s. Closely linked tree-ring growth and net CO ₂ exchange driven by spring temperatures.

Abstract

We investigated long-term (over 100 years) tree-ring width (TRW) variabilities as well as short-term (10 years) variations in net ecosystem productivity (NEP) in response to climate to assess the driving factors for stem growth of Norway spruce in a subalpine forest at Davos in Switzerland. A tree-ring width index (TRWi) chronology for the period from 1750 to 2006 was constructed and linked with climate data from 1876 to 2006, and with NEP available for the period from 1997 to 2006. Based on TRWi, we found that only two out of the 257 years exhibited extreme negative TRWi, compared to 29 years with extreme positive anomalies, observed mainly in recent decades. Annual temperature, annual precipitation, as well as autumn and winter temperature signals were well preserved in the TRWi chronology over the last 130 years. Spring temperatures became increasingly relevant for TRWi, explaining less than 1 % of the variation in TRWi for the period from 1876 to 2006, but 8 % for the period from 1950 to 2006 (p = 0.032), and even 47 % for 1997–2006 (p = 0.028). We also observed a strong positive relationship between annual TRWi and annual NEP (r = 0.661; p = 0.037), both strongly related to spring temperatures (r = 0.687 and r = 0.678 for TRWi and NEP, respectively; p = 0.028; p = 0.032). Moreover, we found strong links between monthly NEP of March and annual TRWi (r = 0.912; p = 0.0001), both related to March temperatures (r = 0.767, p = 0.010 and r = 0.724, p = 0.018, respectively). Thus, under future climate warming, we expect stem growth of these subalpine trees and also ecosystem carbon (C) sequestration to increase, as long as water does not become a limiting factor.     

Representation of aquatic vegetation change by plant macrofossils in a small and shallow freshwater lake

We explored spatial and temporal relationships between contemporary aquatic vegetation and surface sediment macrofossil remains in a small, shallow, English lake (Green Plantation Pond). The aquatic vegetation of Green Plantation Pond underwent a marked compositional change after 2005 with a shift from Elodea spp.-Potamogeton pusillus-Chara spp. to Ceratophyllum spp.-Chara spp.-Potamogeton crispus dominance. By comparing macrophyte and plant macrofossil distributions at multiple, closely spaced points in Green Plantation Pond for 2000 and 2008–2009, we studied the ability of macrofossils to track this major aquatic vegetation change. Representation of macrophytes by macrofossils was high with 63 and 76 % of extant plant species recorded by macro-remains in the 2000 and 2009 sediment surveys respectively. Nevertheless, plants were both over-represented (Nitella flexilis, Chara spp. and Zannichellia palustris) and under-represented (Ranunculus sect. Batrachium, Potamogeton spp.) in the sediment record in terms of relative macrofossil abundances and the number of occupied sample points. The study also revealed a lack of preservation of Elodea spp. leaf remains in the second (2009) survey compared to the first (2000) probably due to a longer time interval (5 vs. 10 months) between macrophyte and sediment sampling. Nevertheless, the macrofossils reliably recorded both the main shift in the contemporary vegetation (e.g. especially increases in Ceratophyllum spp. and P. crispus abundance) and other more subtle floristic changes (e.g. increases in Myriophyllum spicatum and Lemna spp.) exceptionally well. This study highlights the huge potential of macrofossils for tracking sub-decadal changes in the aquatic vegetation of small, shallow lakes.     

A decade of crystallization drops: Crystallization of the cbb3 cytochrome c oxidase from Pseudomonas stutzeri

The cbb₃ cytochrome c oxidases are distant members of the superfamily of heme copper oxidases. These terminal oxidases couple O₂ reduction with proton transport across the plasma membrane and, as a part of the respiratory chain, contribute to the generation of an electrochemical proton gradient. Compared with other structurally characterized members of the heme copper oxidases, the recently determined cbb₃ oxidase structure at 3.2 Å resolution revealed significant differences in the electron supply system, the proton conducting pathways and the coupling of O₂ reduction to proton translocation. In this paper, we present a detailed report on the key steps for structure determination. Improvement of the protein quality was achieved by optimization of the number of lipids attached to the protein as well as the separation of two cbb₃ oxidase isoenzymes. The exchange of n‐dodecyl‐β‐d ‐maltoside for a precisely defined mixture of two α‐maltosides and decanoylsucrose as well as the choice of the crystallization method had a most profound impact on crystal quality. This report highlights problems frequently encountered in membrane protein crystallization and offers meaningful approaches to improve crystal quality.     

Using exomarkers to assess mitochondrial reactive species in vivo

Background

The ability to measure the concentrations of small damaging and signalling molecules such as reactive oxygen species (ROS) in vivo is essential to understanding their biological roles. While a range of methods can be applied to in vitro systems, measuring the levels and relative changes in reactive species in vivo is challenging.

Scope of review

One approach towards achieving this goal is the use of exomarkers. In this, exogenous probe compounds are administered to the intact organism and are then transformed by the reactive molecules in vivo to produce a diagnostic exomarker. The exomarker and the precursor probe can be analysed ex vivo to infer the identity and amounts of the reactive species present in vivo. This is akin to the measurement of biomarkers produced by the interaction of reactive species with endogenous biomolecules.

Major conclusions and general significance

Our laboratories have developed mitochondria-targeted probes that generate exomarkers that can be analysed ex vivo by mass spectrometry to assess levels of reactive species within mitochondria in vivo. We have used one of these compounds, MitoB, to infer the levels of mitochondrial hydrogen peroxide within flies and mice. Here we describe the development of MitoB and expand on this example to discuss how better probes and exomarkers can be developed. This article is part of a Special Issue entitled Current methods to study reactive oxygen species - pros and cons and biophysics of membrane proteins. Guest Editor: Christine Winterbourn.     

Counting glycans revisited

We present an algorithm for counting glycan topologies of order \(n\) that improves on previously described algorithms by a factor \(n\) in both time and space. More generally, we provide such an algorithm for counting rooted or unrooted \(d\) -ary trees with labels or masses assigned to the vertices, and we give a “recipe” to estimate the asymptotic growth of the resulting sequences. We provide constants for the asymptotic growth of \(d\) -ary trees and labeled quaternary trees (glycan topologies). Finally, we show how a classical result from enumeration theory can be used to count glycan structures where edges are labeled by bond types. Our method also improves time bounds for counting alkanes.     

The complex methylome of the human gastric pathogen Helicobacter pylori

The genome of Helicobacter pylori is remarkable for its large number of restriction-modification (R-M) systems, and strain-specific diversity in R-M systems has been suggested to limit natural transformation, the major driving force of genetic diversification in H. pylori. We have determined the comprehensive methylomes of two H. pylori strains at single base resolution, using Single Molecule Real-Time (SMRT®) sequencing. For strains 26695 and J99-R3, 17 and 22 methylated sequence motifs were identified, respectively. For most motifs, almost all sites occurring in the genome were detected as methylated. Twelve novel methylation patterns corresponding to nine recognition sequences were detected (26695, 3; J99-R3, 6). Functional inactivation, correction of frameshifts as well as cloning and expression of candidate methyltransferases (MTases) permitted not only the functional characterization of multiple, yet undescribed, MTases, but also revealed novel features of both Type I and Type II R-M systems, including frameshift-mediated changes of sequence specificity and the interaction of one MTase with two alternative specificity subunits resulting in different methylation patterns. The methylomes of these well-characterized H. pylori strains will provide a valuable resource for future studies investigating the role of H. pylori R-M systems in limiting transformation as well as in gene regulation and host interaction.