The genome-wide identification of pairs of interacting proteins is an important step in the elucidation of cell regulatory mechanisms1,2. Much of our current knowledge derives from high-throughput techniques such as yeast two hybrid and affinity purification3, as well as from manual curation of experiments on individual systems4. A variety of computational approaches based, for example, on sequence homology, gene co-expression, and phylogenetic profiles have also been developed for the genome-wide inference of protein-protein interactions (PPIs)5,6. Yet, comparative studies suggest that the development of accurate and complete repertoires of PPIs is still in its early stages7–9. Here we show that three-dimensional structural information can be used to predict PPIs with an accuracy and coverage that are superior to predictions based on non-structural evidence. Moreover, an algorithm, PrePPI, that combines structural information with other functional clues is comparable in accuracy to high-throughput experiments, yielding over 30,000 high confidence interactions for yeast and over 300,000 for human. Experimental tests of a number of predictions demonstrate the ability of the PrePPI algorithm to identify unexpected PPIs of significant biological interest. The surprising effectiveness of three-dimensional structural information can be attributed to the use of homology models combined with the exploitation of both close and remote geometric relationships between proteins.

To improve chemical cross-linking of proteins coupled with mass spectrometry (CXMS), we developed a lysine-targeted enrichable cross-linker containing a biotin tag for affinity purification, a chemical cleavage site to separate cross-linked peptides away from biotin after enrichment, and a spacer arm that can be labeled with stable isotopes for quantitation. By locating the flexible proteins on the surface of 70S ribosome, we show that this trifunctional cross-linker is effective at attaining structural information not easily attainable by crystallography and electron microscopy. From a crude Rrp46 immunoprecipitate, it helped identify two direct binding partners of Rrp46 and 15 protein-protein interactions (PPIs) among the co-immunoprecipitated exosome subunits. Applying it to E. coli and C. elegans lysates, we identified 3130 and 893 inter-linked lysine pairs, representing 677 and 121 PPIs. Using a quantitative CXMS workflow we demonstrate that it can reveal changes in the reactivity of lysine residues due to protein-nucleic acid interaction.DOI: http://dx.doi.org/10.7554/eLife.12509.001

Low light (LL) is one of the main limiting factors that negatively affect tomato growth and yield. Techniques of chemical regulation are effective horticultural methods to improve stress resistance. Strigolactones (SLs), newly discovered phytohormones, are considered as important regulators of physiological responses. We investigated the effects of foliage spray of GR24, a synthesized SLs, on tomato seedlings grown under LL stress conditions. The results showed that application of GR24 effectively mitigated the inhibition of plant growth and increased the fresh and dry weight of tomato plants under LL. Additionally, GR24 also increased the chlorophyll content (Chl a and Chl b ), the net photosynthetic rate (Pn), the photochemical efficiency of photosystem (PS) II (Fv/Fm), and the effective quantum yield of PSII and I [Y(II) and Y(I)], but decreased the excitation pressure of PSII (1-qP), the non-regulatory quantum yield of energy dissipation [Y(NO)] and the donor side limitation of PSI [Y(ND)] under LL. Moreover, application of GR24 to LL-stressed tomato leaves increased the electron transport rate of PSII and PSI [ETR(II) and ETR(I)], the ratio of the quantum yield of cyclic electron flow (CEF) to Y(II) [Y(CEF)/Y(II)], the oxidized plastoquinone (PQ) pool size and the non-photochemical quenching. Besides, GR24 application increased the activity and gene expression of antioxidant enzymes, but it reduced malonaldehyde (MDA) and hydrogen peroxide (H 2 O 2 ) content in LL-stressed plants. These results suggest that exogenous application of GR24 enhances plant tolerance to LL by promoting plant utilization of light energy to alleviate the photosystem injuries induced by excess light energy and ROS, and enhancing photosynthesis efficiency to improve plant growth.

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The WD-repeat (WDR) proteins comprise an astonishingly diverse superfamily of regulatory proteins. To date, genome-wide characterization of this family has only been conducted in Arabidopsis and little is known about WDR genes in cucumber (Cucumis sativus L.). This study identified 191 cucumber WDR genes in the latest cucumber genome and the CsWDR family contained a smaller number of identified genes compared to Arabidopsis. The results of this study were also supported by genome distribution and gene duplication analysis. Phylogenetic analysis showed that the WDR proteins could be classified into 21 subgroups. Moreover, an additional 12 AtWDR proteins were also identified and a complete overview of this gene family in Arabidopsis is presented, including the phylogeny, chromosome locations and duplication events. In addition, a comparative analysis between these genes in cucumber and Arabidopsis was performed and it suggested that there was strong gene conservation and that there was an expansion of particular functional genes during the evolution of the two species. The transcript abundance level analysis during abiotic stress (NaCl, ABA and low temperature treatments) identified six CsWDR genes that responded to one or more treatments. Tissue-specific expression profiles of these six genes were also analyzed. This study has produced a comparative genomics analysis of the WDR gene family in cucumber and Arabidopsis and provides the first steps towards the selection of CsWDR genes for cloning and functional dissection that can be used in further studies into their roles in cucumber stress resistance.

The solar desalination via interfacial evaporation has shown great potential in addressing the freshwater scarcity issue. However, the evaporation rate and solar thermal conversion efficiency of the current photothermal materials (flat membranes, papers, and thin films) have almost been pushed to the upper limit. In order to further improve the energy efficiency, in this work, we developed a highly porous laser-induced graphene/polyimide (LIG/PI) photothermal membrane with a three-dimensional (3D) architecture through electrospinning and laser ablation techniques. The 3D structure of the LIG/PI membrane increases the evaporation area and reduces the energy loss caused by diffuse reflectance of light. With the assistance of a thermal insulator and water pumping channels, the LIG/PI membrane achieves a high evaporation rate of ∼1.42 kg m–2 h–1, a high solar thermal conversion efficiency of ∼92.55%, and long-term evaporation stability in a high-concentration saline solution under 1 sun illumination. Such a stable photothermal membrane may provide important insights into designing rapid and efficient interfacial evaporation systems.

Background Night-break (NB) has been proven to repress flowering of short-day plants (SDPs). Long-noncoding RNAs (lncRNAs) play key roles in plant flowering. However, investigation of the relationship between lncRNAs and NB responses is still limited, especially in Chenopodium quinoa, an important short-day coarse cereal. Results In this study, we performed strand-specific RNA-seq of leaf samples collected from quinoa seedlings treated by SD and NB. A total of 4914 high-confidence lncRNAs were identified, out of which 91 lncRNAs showed specific responses to SD and NB. Based on the expression profiles, we identified 17 positive- and 7 negative-flowering lncRNAs. Co-expression network analysis indicated that 1653 mRNAs were the common targets of both types of flowering lncRNAs. By mapping these targets to the known flowering pathways in model plants, we found some pivotal flowering homologs, including 2 florigen encoding genes (FT (FLOWERING LOCUS T) and TSF (TWIN SISTER of FT) homologs), 3 circadian clock related genes (EARLY FLOWERING 3 (ELF3), LATE ELONGATED HYPOCOTYL (LHY) and ELONGATED HYPOCOTYL 5 (HY5) homologs), 2 photoreceptor genes (PHYTOCHROME A (PHYA) and CRYPTOCHROME1 (CRY1) homologs), 1 B-BOX type CONSTANS (CO) homolog and 1 RELATED TO ABI3/VP1 (RAV1) homolog, were specifically affected by NB and competed by the positive and negative-flowering lncRNAs. We speculated that these potential flowering lncRNAs may mediate quinoa NB responses by modifying the expression of the floral homologous genes. Conclusions Together, the findings in this study will deepen our understanding of the roles of lncRNAs in NB responses, and provide valuable information for functional characterization in future.

Roots are important plant organs for the absorption of water and nutrients. To date, there have been few genome-wide association studies of maize root system architecture (RSA) in the field. The genetic basis of maize RSA is poorly understood, and the maize RSA-related genes that have been cloned are very limited. Here, 421 maize inbred lines of an association panel were planted to measure the root systems at the maturity stage, and a genome-wide association study was performed. There was a strong correlation among eight RSA traits, and the RSA traits were highly correlated with the aboveground plant architecture traits (e.g., plant height and ear leaf length, r = 0.13–0.25, p < 0.05). The RSA traits of the stiff stalk subgroup (SS) showed lower values than those of the non-stiff stalk subgroup (NSS) and tropical/subtropical subgroup (TST). Using the RSA traits, the genome-wide association study identified 63 SNPs and 189 candidate genes. Among them, nine candidate genes co-localized between RSA and aboveground architecture traits. A further co-expression analysis identified 88 candidate genes having high confidence levels. Furthermore, we identified four highly reliable RSA candidate genes, GRMZM2G099797, GRMZM2G354338, GRMZM2G085042, and GRMZM5G812926. This research provides theoretical support for the genetic improvement of maize root systems, and it identified candidate genes that may act as genetic resources for breeding.