Functionally important segments in proteins dissected using Gene Ontology and geometric clustering of peptide fragments

A geometric clustering algorithm has been developed to dissect protein fragments based on their relevance to function

An Assessment of the Hydrological Trends Using Synergistic Approaches of Remote Sensing and Model Evaluations over Global Arid and Semi-Arid Regions

Drylands cover about 40% of the world’s land area and support two billion people, most of them living in developing countries that are at risk due to land degradation. Over the last few decades, there has been warming, with an escalation of drought and rapid population growth. This will further intensify the risk of desertification, which will seriously affect the local ecological environment, food security and people’s lives. The goal of this research is to analyze the hydrological and land cover characteristics and variability over global arid and semi-arid regions over the last decade (2010–2019) using an integrative approach of remotely sensed and physical process-based numerical modeling (e.g., Global Land Data Assimilation System (GLDAS) and Famine Early Warning Systems Network (FEWS NET) Land Data Assimilation System (FLDAS) models) data. Interaction between hydrological and ecological indicators including precipitation, evapotranspiration, surface soil moisture and vegetation indices are presented in the global four types of arid and semi-arid areas. The trends followed by precipitation, evapotranspiration and surface soil moisture over the decade are also mapped using harmonic analysis. This study also shows that some hotspots in these global drylands, which exhibit different processes of land cover change, demonstrate strong coherency with noted groundwater variations. Various types of statistical measures are computed using the satellite and model derived values over global arid and semi-arid regions. Comparisons between satellite- (NASA-USDA Surface Soil Moisture and MODIS Evapotranspiration data) and model (FLDAS and GLDAS)-derived values over arid regions (BSh, BSk, BWh and BWk) have shown the over and underestimation with low accuracy. Moreover, general consistency is apparent in most of the regions between GLDAS and FLDAS model, while a strong discrepancy is also observed in some regions, especially appearing in the Nile Basin downstream hyper-arid region. Data-driven modelling approaches are thus used to enhance the models’ performance in this region, which shows improved results in multiple statistical measures ((RMSE), bias (ψ), the mean absolute percentage difference (|ψ|)) and the linear regression coefficients (i.e., slope, intercept, and coefficient of determination (R2))

Ribosome–SRP–FtsY cotranslational targeting complex in the closed state

The signal recognition particle (SRP)-dependent pathway is essential for correct targeting of proteins to the membrane and subsequent insertion in the membrane or secretion. In Escherichia coli, the SRP and its receptor FtsY bind to ribosome–nascent chain complexes with signal sequences and undergo a series of distinct conformational changes, which ensures accurate timing and fidelity of protein targeting. Initial recruitment of the SRP receptor FtsY to the SRP–RNC complex results in GTP-independent binding of the SRP–FtsY GTPases at the SRP RNA tetraloop. In the presence of GTP, a closed state is adopted by the SRP–FtsY complex. The cryo-EM structure of the closed state reveals an ordered SRP RNA and SRP M domain with a signal sequence-bound. Van der Waals interactions between the finger loop and ribosomal protein L24 lead to a constricted signal sequence-binding pocket possibly preventing premature release of the signal sequence. Conserved M-domain residues contact ribosomal RNA helices 24 and 59. The SRP–FtsY GTPases are detached from the RNA tetraloop and flexible, thus liberating the ribosomal exit site for binding of the translocation machinery

Structure of a human cap-dependent 48S translation pre-initiation complex

Eukaryotic translation initiation is tightly regulated, requiring a set of conserved initiation factors (eIFs). Translation of a capped mRNA depends on the trimeric eIF4F complex and eIF4B to load the mRNA onto the 43S pre-initiation complex comprising 40S and initiation factors 1, 1A, 2, 3 and 5 as well as initiator-tRNA. Binding of the mRNA is followed by mRNA scanning in the 48S pre-initiation complex, until a start codon is recognised. Here, we use a reconstituted system to prepare human 48S complexes assembled on capped mRNA in the presence of eIF4B and eIF4F. The highly purified h-48S complexes are used for cross-linking/mass spectrometry, revealing the protein interaction network in this complex. We report the electron cryo-microscopy structure of the h-48S complex at 6.3 Å resolution. While the majority of eIF4B and eIF4F appear to be flexible with respect to the ribosome, additional density is detected at the entrance of the 40S mRNA channel which we attribute to the RNA-recognition motif of eIF4B. The eight core subunits of eIF3 are bound at the 40S solvent-exposed side, as well as the subunits eIF3d, eIF3b and eIF3i. elF2 and initiator-tRNA bound to the start codon are present at the 40S intersubunit side. This cryo-EM structure represents a molecular snap-shot revealing the h-48S complex following start codon recognition

A central cavity within the holo-translocon suggests a mechanism for membrane protein insertion.

The conserved SecYEG protein-conducting channel and the accessory proteins SecDF-YajC and YidC constitute the bacterial holo-translocon (HTL), capable of protein-secretion and membrane-protein insertion. By employing an integrative approach combining small-angle neutron scattering (SANS), low-resolution electron microscopy and biophysical analyses we determined the arrangement of the proteins and lipids within the super-complex. The results guided the placement of X-ray structures of individual HTL components and allowed the proposal of a model of the functional translocon. Their arrangement around a central lipid-containing pool conveys an unexpected, but compelling mechanism for membrane-protein insertion. The periplasmic domains of YidC and SecD are poised at the protein-channel exit-site of SecY, presumably to aid the emergence of translocating polypeptides. The SecY lateral gate for membrane-insertion is adjacent to the membrane 'insertase' YidC. Absolute-scale SANS employing a novel contrast-match-point analysis revealed a dynamic complex adopting open and compact configurations around an adaptable central lipid-filled chamber, wherein polytopic membrane-proteins could fold, sheltered from aggregation and proteolysis

Advancing ecological assessment of the Arabian Gulf through eDNA metabarcoding: opportunities, prospects, and challenges

The Arabian Gulf (hereafter ‘the Gulf’) is renowned for its unique ecological characteristics and distinct marine life. It offers a diverse range of ecosystems that have adapted to the impacts posed by natural stress and human activities. Regular biomonitoring and diversity assessments are necessary to document the health of the Gulf ecosystem and to implement appropriate measures for effective conservation and management. Recently, environmental DNA (eDNA), a total pool of DNA isolated from environmental samples, has emerged as a highly effective tool for ecological studies. This review explores the opportunities, prospects, and challenges associated with employing eDNA metabarcoding in the ecological assessment and biomonitoring of the Gulf. It provides an overview of the status of the Gulf ecosystem and discusses the potential applications of eDNA metabarcoding in assessing biodiversity, monitoring invasive species, and evaluating ecosystem health. Additionally, the investigation addresses the challenges inherent in implementing this technique, considering environmental complexities, methodological intricacies, and data interpretation. Overall, this review emphasizes the immense potential of eDNA metabarcoding in advancing ecological assessment in the Gulf and calls for further research and collaboration to harness its benefits in this unique marine ecosystem

Structural basis of signal sequence surveillance and selection by the SRP–FtsY complex

Signal-recognition particle (SRP)-dependent targeting of translating ribosomes to membranes is a multistep quality-control process. Ribosomes that are translating weakly hydrophobic signal sequences can be rejected from the targeting reaction even after they are bound to the SRP. Here we show that the early complex, formed by Escherichia coli SRP and its receptor FtsY with ribosomes translating the incorrect cargo EspP, is unstable and rearranges inefficiently into subsequent conformational states, such that FtsY dissociation is favored over successful targeting. The N-terminal extension of EspP is responsible for these defects in the early targeting complex. The cryo-electron microscopy structure of this 'false' early complex with EspP revealed an ordered M domain of SRP protein Ffh making two ribosomal contacts, and the NG domains of Ffh and FtsY forming a distorted, flexible heterodimer. Our results provide a structural basis for SRP-mediated signal-sequence selection during recruitment of the SRP receptor