Identification of miRNA858 long-loop precursors in seed plants.

MicroRNAs (miRNAs) are a class of nonprotein-coding short transcripts that provide a layer of post-transcriptional regulation essential to many plant biological processes. MiR858, which targets the transcripts of MYB transcription factors, can affect a range of secondary metabolic processes. Although miR858 and its 187-nt precursor have been well studied in Arabidopsis (Arabidopsis thaliana), a systematic investigation of miR858 precursors and their functions across plant species is lacking due to a problem in identifying the transcripts that generate this subclass. By re-evaluating the transcript of miR858 and relaxing the length cut-off for identifying hairpins, we found in kiwifruit (Actinidia chinensis) that miR858 has long-loop hairpins (1,100 to 2,100 nt), whose intervening sequences between miRNA generating complementary sites were longer than all previously reported miRNA hairpins. Importantly, these precursors of miR858 containing long-loop hairpins (termed MIR858L) are widespread in seed plants including Arabidopsis, varying between 350 and 5,500 nt. Moreover, we showed that MIR858L has a greater impact on proanthocyanidin and flavonol levels in both Arabidopsis and kiwifruit. We suggest that an active MIR858L-MYB regulatory module appeared in the transition of early land plants to large upright flowering plants, making a key contribution to plant secondary metabolism.

An LRH-RSL4 feedback regulatory loop controls the determinate growth of root hairs in Arabidopsis.

Root hairs are tubular-shaped outgrowths of epidermal cells essential for plants acquiring water and nutrients from the soil. Despite their importance, the growth of root hairs is finite. How this determinate growth is precisely regulated remains largely unknown. Here we identify LONG ROOT HAIR (LRH), a GYF domain-containing protein, as a unique repressor of root hair growth. We show that LRH inhibits the association of eukaryotic translation initiation factor 4Es (eIF4Es) with the mRNA of ROOT HAIR DEFECTIVE6-LIKE4 (RSL4) that encodes the master regulator of root hair growth, repressing RSL4 translation and thus root hair elongation. RSL4 in turn directly transactivates LRH expression to maintain a proper LRH gradient in the trichoblasts. Our findings reveal a previously uncharacterized LRH-RSL4 feedback regulatory loop that limits root hair growth, shedding new light on the mechanism underlying the determinate growth of root hairs.

A competition-attenuation mechanism modulates thermoresponsive growth at warm temperatures in plants.

Global warming has profound impact on growth and development, and plants constantly adjust their internal circadian clock to cope with external environment. However, how clock-associated genes fine-tune thermoresponsive growth in plants is little understood. We found that loss-of-function mutation of REVEILLE5 (RVE5) reduces the expression of circadian gene EARLY FLOWERING 4 (ELF4) in Arabidopsis, and confers accelerated hypocotyl growth under warm-temperature conditions. Both RVE5 and CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) accumulate at warm temperatures and bind to the same EE cis-element presented on ELF4 promoter, but the transcriptional repression activity of RVE5 is weaker than that of CCA1. The binding of CCA1 to ELF4 promoter is enhanced in the rve5-2 mutant at warm temperatures, and overexpression of ELF4 in the rve5-2 mutant background suppresses the rve5-2 mutant phenotype at warm temperatures. Therefore, the transcriptional repressor RVE5 finetunes ELF4 expression via competing at a cis-element with the stronger transcriptional repressor CCA1 at warm temperatures. Such a competition-attenuation mechanism provides a balancing system for modulating the level of ELF4 and thermoresponsive hypocotyl growth under warm-temperature conditions.

Integration of bio-inspired lanthanide-transition metal cluster and P-doped carbon nitride for efficient photocatalytic overall water splitting.

Photosynthesis in nature uses the Mn4CaO5 cluster as the oxygen-evolving center to catalyze the water oxidation efficiently in photosystem II. Herein, we demonstrate bio-inspired heterometallic LnCo3 (Ln = Nd, Eu and Ce) clusters, which can be viewed as synthetic analogs of the CaMn4O5 cluster. Anchoring LnCo3 on phosphorus-doped graphitic carbon nitrides (PCN) shows efficient overall water splitting without any sacrificial reagents. The NdCo3/PCN-c photocatalyst exhibits excellent water splitting activity and a quantum efficiency of 2.0% at 350 nm. Ultrafast transient absorption spectroscopy revealed the transfer of a photoexcited electron and hole into the PCN and LnCo3 for hydrogen and oxygen evolution reactions, respectively. A density functional theory (DFT) calculation showed the cooperative water activation on lanthanide and O-O bond formation on transition metal for water oxidation. This work not only prepares a synthetic model of a bio-inspired oxygen-evolving center but also provides an effective strategy to realize light-driven overall water splitting.

Polyethylene film mulching enhances the microbial carbon-use efficiency, physical and chemical protection of straw-derived carbon in an Entisol of the Loess Plateau.

The global use of agricultural polyethylene mulches has emerged as a widespread farming practice, however, its effects on the fate and dynamics of crop straw-derived C in soil microbial biomass C (MBC), aggregate-associated and chemical recalcitrance-related C fractions are rarely assessed in situ. A two-year field experiment using 13C-labeled maize stem was carried out to quantify the allocation and dynamics of straw-C in an Entisol with and without plastic mulching. The results indicated that across the treatments, from 49.2% to 56.4% of straw-13C was released as CO2-C, from 34.9% to 43.1% was sequestrated as SOC pool, and from 6.7% to 9.7% remained undecomposed at the end of the experiment. Compared to non-mulching, plastic mulching significantly decreased the straw-derived CO2-C emissions by 14.6%, partially owing to the increased incorporation of straw-C into SOC pool. Across the treatments, the straw-derived MBC ranged from 14.4 to 147.9 mg 13C kg-1; and plastic mulching increased straw-derived MBC and microbial C use efficiency (CUE) of straw residue by 41.2% and 35.2% compared with non-mulching, respectively. The allocation dynamics of straw-C in each soil aggregate followed a sustained upward trend with time, while a significantly higher straw-C was incorporated into both macro- (> 0.25 mm) and micro-aggregates (0.25-0.053 mm) with plastic mulching. Compared to the non-mulching, plastic mulching enhanced the inclusion of straw-13C in the chimerically more stable C fraction, especially at the late experimental period. We conclude that crop straw return combined with plastic mulching could improve SOC sequestration by enhancing microbial CUE, physical and chemical protection of straw-derived C in this dryland cropping system.

Therapeutic Potential and Biological Applications of Cordycepin and Metabolic Mechanisms in Cordycepin-Producing Fungi.

Cordycepin(3'-deoxyadenosine), a cytotoxic nucleoside analogue found in Cordyceps militaris, has attracted much attention due to its therapeutic potential and biological value. Cordycepin interacts with multiple medicinal targets associated with cancer, tumor, inflammation, oxidant, polyadenylation of mRNA, etc. The investigation of the medicinal drug actions supports the discovery of novel targets and the development of new drugs to enhance the therapeutic potency and reduce toxicity. Cordycepin may be of great value owing to its medicinal potential as an external drug, such as in cosmeceutical, traumatic, antalgic and muscle strain applications. In addition, the biological application of cordycepin, for example, as a ligand, has been used to uncover molecular structures. Notably, studies that investigated the metabolic mechanisms of cordycepin-producing fungi have yielded significant information related to the biosynthesis of high levels of cordycepin. Here, we summarized the medicinal targets, biological applications, cytotoxicity, delivery carriers, stability, and pros/cons of cordycepin in clinical applications, as well as described the metabolic mechanisms of cordycepin in cordycepin-producing fungi. We posit that new approaches, including single-cell analysis, have the potential to enhance medicinal potency and unravel all facets of metabolic mechanisms of cordycepin in Cordyceps militaris.

A Phosphate-Starvation Induced RING-Type E3 Ligase Maintains Phosphate Homeostasis Partially Through OsSPX2 in Rice.

Phosphate (Pi), as the main form of phosphorus that can be absorbed by plants, is one of the most limiting macro-nutrients for plants. However, the mechanism for maintaining Pi homeostasis in rice (Oryza sativa) is still not well understood. We identified a Pi-starvation-induced E3 ligase (OsPIE1) in rice. Using an in vitro self-ubiquitination assay, we determined the E3 ligase activities of OsPIE1. Using GUS staining and GFP detection, we analyzed tissue expression patterns of OsPIE1 and the subcellular localization of its encoded protein. The function of OsPIE1 in Pi homeostasis was analyzed using OsPIE1 overexpressors and ospie1 mutants. OsPIE1 was localized to the nucleus, and expressed in epidermis, exodermis and sclerenchyma layers of primary root. Under Pi-sufficient condition, overexpression of OsPIE1 upregulated the expression of OsPT2, OsPT3, OsPT10 and OsPAP21b, resulting in Pi accumulation and acid phosphatases (APases) induction in roots. OsSPX2 was strongly suppressed in OsPIE1 overexpressors. Further comparative transcriptome analysis, tissue expression patterns and genetic interaction analysis indicated that the enhancing of Pi accumulation and APase activities upon overexpression of OsPIE1 was (at least in part) caused by repression of OsSPX2. These results indicate that OsPIE1 plays an important role in maintaining Pi homeostasis in rice.

Characterization of natural co-cultures of Piromyces with Methanobrevibacter ruminantium from yaks grazing on the Qinghai-Tibetan Plateau: a microbial consortium with high potential in plant biomass degradation.

Anaerobic fungi reside in the gut of herbivore and synergize with associated methanogenic archaea to decompose ingested plant biomass. Despite their potential for use in bioconversion industry, only a few natural fungus-methanogen co-cultures have been isolated and characterized. In this study we identified three co-cultures of Piromyces with Methanobrevibacter ruminantium from the rumen of yaks grazing on the Qinghai Tibetan Plateau. The representative co-culture, namely (Piromyces + M. ruminantium) Yak-G18, showed remarkable polysaccharide hydrolase production, especially xylanase. Consequently, it was able to degrade various lignocellulose substrates with a biodegrading capability superior to most previously identified fungus or fungus-methanogen co-culture isolates. End-product profiling analysis validated the beneficial metabolic impact of associated methanogen on fungus as revealed by high-yield production of methane and acetate and sustained growth on lignocellulose. Together, our data demonstrated a great potential of (Piromyces + M. ruminantium) Yak-G18 co-culture for use in industrial bioconversion of lignocellulosic biomass.

Fiber degradation potential of natural co-cultures of Neocallimastix frontalis and Methanobrevibacter ruminantium isolated from yaks (Bos grunniens) grazing on the Qinghai Tibetan Plateau.

Several natural anaerobic fungus-methanogen co-cultures have been isolated from rumen and feces source of herbivores with strong fiber degrading ability. In this study, we isolated 7 Neocallimastix with methanogen co-cultures from the rumen of yaks grazing on the Qinghai Tibetan Plateau. Based on morphological characteristics and internal transcribed spacer 1 sequences (ITS1), all the fungi were identified as Neocallimastix frontalis. The co-cultures were confirmed as the one fungus - one methanogen pattern by the PCR-denatured gradient gel electrophoresis (DGGE) assay. All the methanogens were identified as Methanobrevibacter ruminantium by 16s rRNA gene sequencing. We investigated the biodegrading capacity of the co-culture (N. frontalis + M. ruminantium) Yaktz1 on wheat straw, corn stalk and rice straw in a 7 days-incubation. The in vitro dry matter digestibility (IVDMD), acid detergent fiber digestibility (ADFD) and neural detergent fiber digestibility (NDFD) values of the substrates in the co-culture were significantly higher than those in the mono-culture N. frontalis Yaktz1. The co-culture exhibited high polysaccharide hydrolase (xylanase and FPase) and esterase activities. The xylanase in the co-culture reached the highest activity of 12500 mU/ml on wheat straw at the day 3 of the incubation. At the end of the incubation, 3.00 mmol-3.29 mmol/g dry matter of methane were produced by the co-culture. The co-culture also produced high level of acetate (40.00 mM-45.98 mM) as the end-product during the biodegradation. Interestingly, the N. frontalis Yaktz1 mono-culture produced large amount of lactate (8.27 mM-11.60 mM) and ethanol (163.11 mM-242.14 mM), many times more than those recorded in the previously reported anaerobic fungi. Our data suggests that the (N. frontalis + M. ruminantium) Yaktz1 co-culture and the N. frontalis Yaktz1 mono-culture both have great potentials for different industrial use.

[Microbial diversity analysis in rotating drum biofilter for nitric oxide denitrifying removal].

PCR-DGGE was applied to analyze the microbial communities in rotating drum biofilter (RDB) for nitric oxide denitrifying removal under anaerobic conditions. The 16S rRNA genes (V3 region) were amplified with two universal primers (338F-GC and 518R). These amplified DNA fragments were separated by parallel DGGE. The DGGE profiles of biofilm samples from different sections of RDB are similar and about sixteen types of microorganisms are identified in the biofilm samples. These results show that microbial diversity of RDB firstly increases but then decreases with the addition of Cu II (EDTA) and the increase of NO removal efficiency. However, the change of microbial community is not significant during the process. Eight major bands of 16S rRNA genes fragments from DGGE profiles of biofilm samples were further eluted from gel, re-amplified, cloned and sequenced. The sequences of these fragments were compared with the database in GeneBank (NCBI). The gene analysis of 16S rRNA showed that the major populations are Cytopahga-Flexibacteria-Bacteroides (CFB) group Bacteroides, beta -Proteobacterium, gamma-Proteobacterium and Clostridium sp.. In addition, denitrification is related with band G-5, G-6 and G-8. G-5 is affiliated with gamma-Proteobacterium. Both G-6 and G-8 are affiliated with beta-Proteobacterium.