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CCR4-NOT is a conserved multiprotein complex which regulates eukaryotic gene expression principally via shortening of poly(A) tails of messenger RNA or deadenylation. Here, we reconstitute a complete, recombinant human CCR4-NOT complex. Our reconstitution strategy permits strict compositional control to test mechanistic hypotheses with purified component variants. CCR4-NOT is more active and selective for poly(A) than the isolated exonucleases, CCR4a and CAF1, which have distinct deadenylation profiles in vitro. The exonucleases require at least two out of three conserved non-enzymatic modules (CAF40, NOT10:NOT11 or NOT) for full activity in CCR4-NOT. CAF40 and the NOT10:NOT11 module both bind RNA directly and stimulate deadenylation in a partially redundant manner. Linear motifs from different RNA-binding factors that recruit CCR4-NOT to specific mRNAs via protein-protein interactions with CAF40 can inhibit bulk deadenylation. We reveal an additional layer of regulatory complexity to the human deadenylation machinery, which may prime it either for general or target-specific degradation. The CCR4-NOT complex shortens poly(A) tails of messenger RNAs. By biochemical reconstitution of the entire human CCR4-NOT complex, the authors show the stimulatory roles of non-enzymatic subunits and the importance of the interaction between CAF40 and RNA binding proteins in targeted deadenylation.

Recent findings indicate that the translation elongation rate influences mRNA stability. One of the factors that has been implicated in this link between mRNA decay and translation speed is the yeast DEAD-box helicase Dhh1p. Here, we demonstrated that the human ortholog of Dhh1p, DDX6, triggers the deadenylation-dependent decay of inefficiently translated mRNAs in human cells. DDX6 interacts with the ribosome through the Phe-Asp-Phe (FDF) motif in its RecA2 domain. Furthermore, RecA2-mediated interactions and ATPase activity are both required for DDX6 to destabilize inefficiently translated mRNAs. Using ribosome profiling and RNA sequencing, we identified two classes of endogenous mRNAs that are regulated in a DDX6-dependent manner. The identified targets are either translationally regulated or regulated at the steady-state-level and either exhibit signatures of poor overall translation or of locally reduced ribosome translocation rates. Transferring the identified sequence stretches into a reporter mRNA caused translation- and DDX6-dependent degradation of the reporter mRNA. In summary, these results identify DDX6 as a crucial regulator of mRNA translation and decay triggered by slow ribosome movement and provide insights into the mechanism by which DDX6 destabilizes inefficiently translated mRNAs.

This study utilized the North American PhenoCam network to evaluate phenological characteristics and their relationships with geographic and climatic factors across deciduous broadleaf (n = 39) and evergreen needleleaf (n = 13) forests over the past decade. Using high temporal resolution near-surface imagery, key phenological indicators including the start, end, and length of growing season were derived and analyzed using linear regression and structural equation modeling. The results revealed substantial spatial variation; the evergreen needleleaf sites exhibited earlier starts to the growing season (112 vs. 130 Julian date), later ends to the growing season (286 vs. 264 Julian date), and longer lengths for the growing season (172 vs. 131 days) compared with the deciduous broadleaf sites. Latitude was significantly related to the start of the growing season and the length of the growing season at the deciduous broadleaf sites (R2 = 0.28–0.41, p < 0.01), while these relationships were weaker at the evergreen needleleaf sites, and elevation had mixed effects. The mean annual temperature strongly influenced the phenology for both forest types (R2 = 0.18–0.76, p < 0.01), whereas longitude, distance to the coast, and precipitation had negligible effects. Temporal trends in the phenological indicators were sporadic across both the deciduous broadleaf and evergreen needleleaf sites. Structural equation modeling revealed distinct causal pathways for each forest type, highlighting complex interactions among the geographical and climatic variables. At the deciduous broadleaf sites, geographical factors (latitude, elevation, and distance to the nearest coast) predominated the mean annual temperature, which in turn significantly affected phenological development (χ2 = 2.171, p = 0.975). At the evergreen needleleaf sites, geographical variables had more complex effects on the climatic factors, start of the growing season, and end of the growing season, with the end of the growing season emerging as the primary determinant of growing season length (χ2 = 0.486, p = 0.784). The PhenoCam network provides valuable fine-scale phenological dynamics, offering great insights for forest management, biodiversity conservation, and understanding carbon cycling under climate change.

Vegetation phenology is an integrative indicator of environmental change, and remotely–sensed data provide a powerful way to monitor land surface vegetation responses to climatic fluctuations across various spatiotemporal scales. In this study, we synthesize the local climate, mainly temperature and precipitation, and large-scale atmospheric anomalies, El Niño-Southern Oscillation (ENSO)-connected dynamics, on a vegetative surface in a subtropical mountainous island, the northwest Pacific of Taiwan. We used two decadal photosynthetically active vegetation cover (PV) data (2001–2020) from Moderate Resolution Imaging Spectroradiometer (MODIS) reflectance data to portray vegetation dynamics at monthly, seasonal, and annual scales. Results show that PV is positively related to both temperature and precipitation at a monthly timescale across various land cover types, and the log-linear with one-month lagged of precipitation reveals the accumulation of seasonal rainfall having a significant effect on vegetation growth. Using TIMESAT, three annual phenological metrics, SOS (start of growing season), EOS (end of growing season), and LOS (length of growing season), have been derived from PV time series and been related to seasonal rainfall. The delayed SOS was manifestly influenced by a spring drought, <40 mm during February–March. The later SOS led to a ramification on following late EOS, shorter LOS, and reduction of annual NPP. Nevertheless, the summer rainfall (August–October) and EOS had no significant effects on vegetation growth owing to abundant rainfall. Therefore, the SOS associated with spring rainfall, instead of EOS, played an advantageous role in regulating vegetation development in this subtropical island. The PCA (principal component analysis) was applied for PV time series and explored the spatiotemporal patterns connected to local climate and climatic fluctuations for entire Taiwan, North Taiwan, and South Taiwan. The first two components, PC1 and PC2, explained most of data variance (94–95%) linked to temporal dynamics of land cover (r > 0.90) which was also regulated by local climate. While the subtle signals of PC3 and PC4 explained 0.1–0.4% of the data variance, related to regional drought (r = 0.35–0.40) especially in central and southwest Taiwan and ENSO-associated rainfall variation (r = −0.40–−0.37). Through synthesizing the relationships between vegetation dynamics and climate based on multiple timescales, there will be a comprehensive picture of vegetation growth and its cascading effects on ecosystem productivity.

Forests are the most important component of terrestrial ecosystem; the accurate mapping of tree species is helpful for the management of forestry resources. Moderate- and high-resolution multispectral images have been commonly utilized to identify regional tree species in forest ecosystem, but the accuracy of recognition is still unsatisfactory. To enhance the forest mapping accuracy, this study integrated the land surface phenological metrics and text features of forest canopy on tree species identification based on Gaofen-1 (GF-1) wide field of view (WFV) and time-series images (36 10-day NDVI data), conducted at a forested landscape in Harqin Banner, Northeast China in 2017. The dominant tree species include Pinus tabulaeformis, Larix gmelinii, Populus davidiana, Betula platyphylla, and Quercus mongolica in the study region. The result of forest mapping derived from a 10-day dataset was also compared with the outcome based upon a commonly utilized 30-day dataset in tree species identification. The results indicate that tree species identification accuracy is significantly (p < 0.05) improved with higher temporal resolution (10-day, 79.4%) of images than commonly used monthly data (30-day, 76.14%), and the accuracy can be further increased to 85.13% with a combination of the information derived from principal component analysis (PCA) transformation, phenological metrics (standing for the information of growing season) and texture features. The integration of higher dimensional NDVI data, vegetation growth dynamics and feature of canopy simultaneously will be beneficial to map tree species at the landscape scale.

Vegetation phenology, i [...]

The TREX complex couples nuclear pre‐mRNA processing with mRNA export and contains multiple protein components, including Uap56, Alyref, Cip29 and the multi‐subunit THO complex. Here, we have identified Chtop as a novel TREX component. We show that both Chtop and Alyref activate the ATPase and RNA helicase activities of Uap56 and that Uap56 functions to recruit both Alyref and Chtop onto mRNA. As observed with the THO complex subunit Thoc5, Chtop binds to the NTF2‐like domain of Nxf1, and this interaction requires arginine methylation of Chtop. Using RNAi, we show that co‐knockdown of Alyref and Chtop results in a potent mRNA export block. Chtop binds to Uap56 in a mutually exclusive manner with Alyref, and Chtop binds to Nxf1 in a mutually exclusive manner with Thoc5. However, Chtop, Thoc5 and Nxf1 exist in a single complex in vivo . Together, our data indicate that TREX and Nxf1 undergo dynamic remodelling, driven by the ATPase cycle of Uap56 and post‐translational modifications of Chtop. The TREX complex coordinates nuclear mRNA processing and export. Chtop is a novel TREX component that stimulates the helicase activity of Uap56 and mediates Nxf1 binding to dynamically remodel mRNP export complexes.

Due to their destructive and sporadic nature, it is often difficult to evaluate and predict the effects of typhoon on forest ecosystem patterns and processes. We used a 21-yr record of litterfall rates to explore the influence of typhoon frequency and intensity, along with other meteorological variables, on ecosystem dynamics in a subtropical rainforest. Over the past half century there has been an increasing frequency of strong typhoons (category 3; >49.6 m s −1 ; increase of 1.5 typhoons/decade) impacting the Fushan Experimental Forest, Taiwan. At Fushan strong typhoons drive total litterfall mass with an average of 1100 kg ha −1 litterfall typhoon −1 . While mean typhoon season litterfall has been observed to vary by an order of magnitude, mean litterfall rates associated with annual leaf senescence vary by <20%. In response to increasing typhoon frequency, total annual litter mass increased gradually over the 21-year record following three major typhoons in 1994. Monthly maximum wind speed was predictive of monthly litterfall, yet the influence of precipitation and temperature was only evident in non-typhoon affected months. The response of this subtropical forest to strong typhoons suggests that increasing typhoon frequency has already shifted ecosystem structure and function (declining carbon sequestration and forest stature).

The metazoan TREX complex is recruited to mRNA during nuclear RNA processing and functions in exporting mRNA to the cytoplasm. Nxf1 is an mRNA export receptor, which binds processed mRNA and transports it through the nuclear pore complex. At present, the relationship between TREX and Nxf1 is not understood. Here we show that Nxf1 uses an intramolecular interaction to inhibit its own RNA-binding activity. When the TREX subunits Aly and Thoc5 make contact with Nxf1, Nxf1 is driven into an open conformation, exposing its RNA-binding domain, allowing RNA binding. Moreover, the combined knockdown of Aly and Thoc5 markedly reduces the amount of Nxf1 bound to mRNA in vivo and also causes a severe mRNA export block. Together, our data indicate that TREX provides a license for mRNA export by driving Nxf1 into a conformation capable of binding mRNA. The TREX complex and Nxf1 are involved in the export of mRNA from the nucleus but the precise molecular function of TREX is unclear. Here, the TREX components Aly and Thoc5 are shown to bind to Nxf1 resulting in a change in Nxf1 conformation that permits binding to mRNA and nuclear export.

The removal of the mRNA 5′ cap structure by the decapping enzyme DCP2 leads to rapid 5′→3′ mRNA degradation by XRN1, suggesting that the two processes are coordinated. Biochemical and structural analyses now reveal a molecular basis for this coupling by showing that XRN1 directly interacts with the decapping activators EDC4 and DCP1 in human and Drosophila melanogaster cells, respectively. The removal of the mRNA 5′ cap structure by the decapping enzyme DCP2 leads to rapid 5′→3′ mRNA degradation by XRN1, suggesting that the two processes are coordinated, but the coupling mechanism is unknown. DCP2 associates with the decapping activators EDC4 and DCP1. Here we show that XRN1 directly interacts with EDC4 and DCP1 in human and Drosophila melanogaster cells, respectively. In D. melanogaster cells, this interaction is mediated by the DCP1 EVH1 domain and a DCP1-binding motif (DBM) in the XRN1 C-terminal region. The NMR structure of the DCP1 EVH1 domain bound to the DBM reveals that the peptide docks at a conserved aromatic cleft, which is used by EVH1 domains to recognize proline-rich ligands. Our findings reveal a role for XRN1 in decapping and provide a molecular basis for the coupling of decapping to 5′→3′ mRNA degradation.