Dataset Information

Structural characterization of NrnC identifies unifying features of dinucleotidases.

ABSTRACT: RNA degradation is fundamental for cellular homeostasis. The process is carried out by various classes of endolytic and exolytic enzymes that together degrade an RNA polymer to mono-ribonucleotides. Within the exoribonucleases, nano-RNases play a unique role as they act on the smallest breakdown products and hence catalyze the final steps in the process. We recently showed that oligoribonuclease (Orn) acts as a dedicated diribonucleotidase, defining the ultimate step in RNA degradation that is crucial for cellular fitness (Kim et al., 2019). Whether such a specific activity exists in organisms that lack Orn-type exoribonucleases remained unclear. Through quantitative structure-function analyses, we show here that NrnC-type RNases share this narrow substrate length preference with Orn. Although NrnC and Orn employ similar structural features that distinguish these two classes of dinucleotidases from other exonucleases, the key determinants for dinucleotidase activity are realized through distinct structural scaffolds. The structures, together with comparative genomic analyses of the phylogeny of DEDD-type exoribonucleases, indicate convergent evolution as the mechanism of how dinucleotidase activity emerged repeatedly in various organisms. The evolutionary pressure to maintain dinucleotidase activity further underlines the important role these analogous proteins play for cell growth.

SUBMITTER: Lormand JD

PROVIDER: S-EPMC8492067 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Structural characterization of NrnC identifies unifying features of dinucleotidases.

Lormand Justin D JD Kim Soo-Kyoung SK Walters-Marrah George A GA Brownfield Bryce A BA Fromme J Christopher JC Winkler Wade C WC Goodson Jonathan R JR Lee Vincent T VT Sondermann Holger H

eLife 20210917

RNA degradation is fundamental for cellular homeostasis. The process is carried out by various classes of endolytic and exolytic enzymes that together degrade an RNA polymer to mono-ribonucleotides. Within the exoribonucleases, nano-RNases play a unique role as they act on the smallest breakdown products and hence catalyze the final steps in the process. We recently showed that oligoribonuclease (Orn) acts as a dedicated diribonucleotidase, defining the ultimate step in RNA degradation that is c ...[more]

PMID: 34533457

Similar Datasets

Project description:BACKGROUND:Nucleosome distribution along chromatin dictates genomic DNA accessibility and thus profoundly influences gene expression. However, the underlying mechanism of nucleosome formation remains elusive. Here, taking a structural perspective, we systematically explored nucleosome formation potential of genomic sequences and the effect on chromatin organization and gene expression in S. cerevisiae. RESULTS:We analyzed twelve structural features related to flexibility, curvature and energy of DNA sequences. The results showed that some structural features such as DNA denaturation, DNA-bending stiffness, Stacking energy, Z-DNA, Propeller twist and free energy, were highly correlated with in vitro and in vivo nucleosome occupancy. Specifically, they can be classified into two classes, one positively and the other negatively correlated with nucleosome occupancy. These two kinds of structural features facilitated nucleosome binding in centromere regions and repressed nucleosome formation in the promoter regions of protein-coding genes to mediate transcriptional regulation. Based on these analyses, we integrated all twelve structural features in a model to predict more accurately nucleosome occupancy in vivo than the existing methods that mainly depend on sequence compositional features. Furthermore, we developed a novel approach, named DLaNe, that located nucleosomes by detecting peaks of structural profiles, and built a meta predictor to integrate information from different structural features. As a comparison, we also constructed a hidden Markov model (HMM) to locate nucleosomes based on the profiles of these structural features. The result showed that the meta DLaNe and HMM-based method performed better than the existing methods, demonstrating the power of these structural features in predicting nucleosome positions. CONCLUSIONS:Our analysis revealed that DNA structures significantly contribute to nucleosome organization and influence chromatin structure and gene expression regulation. The results indicated that our proposed methods are effective in predicting nucleosome occupancy and positions and that these structural features are highly predictive of nucleosome organization.The implementation of our DLaNe method based on structural features is available online.

Project description:ImportanceThere is a strong and increasing focus on redressing structural racism in health care systems. Structural racism persists by separating clinical care sites that treat patients of racial and ethnic minority groups who are disproportionately covered by Medicaid from sites that treat patients who are White and disproportionately covered by commercial insurance. Practice unification refers to efforts to eliminate this form of segregation.ObjectiveTo define and investigate the facilitators, barriers, and the effects associated with unification of outpatient practices to reduce structural racism in a large urban health system.Design, setting, and participantsThis qualitative study used semistructured interviews conducted within a large urban health system in New York from February to October 2023. Trained researchers interviewed clinical and administrative leaders of outpatient clinical practices that were pursuing unification, and health system leaders overseeing multiple practices.Main outcomes and measuresThematic analysis was used to identify facilitators of and barriers to unification, challenges and benefits after unification, and persistent dimensions of segregation within clinics that had nominally unified. These insights were used to create a framework for the unification process.ResultsThe thematic analysis included qualitative information from 5 administrative leaders, 12 clinical leaders, and 6 health system leaders, and found that unification facilitators were financial benefit, relocation to new facility spaces, and advocacy by leaders and trainees, while barriers were financial concerns, space constraints, and physician and staff attitudes. After attaining and experiencing some degree of practice unification, interviewees reported financial gain, more support staff, perceptions of greater equity, better educational experiences, and increased practitioner and trainee satisfaction. Challenges reported after unification were changes in staff roles, financial concerns, patient dissatisfaction, and difficulties interfacing with segregated practices within the health system. Partially unified practices maintained dimensions of segregation, by practitioner, payer, and/or scheduling/time (temporal segregation).Conclusions and relevanceThis qualitative study found that outpatient practice unification was perceived to be a financially and equity-driven process with multiple dimensions. However, not all of the unification procedures had been completely implemented. These findings indicate that successful unification of outpatient practices in a large urban health care system requires attention to multiple dimensions, as well as overcoming challenges regarding finances, facility space, reimbursement policies, and patient and staff satisfaction.

Project description:MHC class II molecules (MHC II) play a pivotal role in the cell-surface presentation of antigens for surveillance by T cells. Antigen loading takes place inside the cell in endosomal compartments and loss of the peptide ligand rapidly leads to the formation of a non-receptive state of the MHC molecule. Non-receptiveness hinders the efficient loading of new antigens onto the empty MHC II. However, the mechanisms driving the formation of the peptide inaccessible state are not well understood. Here, a combined approach of experimental site-directed mutagenesis and computational modeling is used to reveal structural features underlying "non-receptiveness." Molecular dynamics simulations of the human MHC II HLA-DR1 suggest a straightening of the ?-helix of the ?1 domain during the transition from the open to the non-receptive state. The movement is mostly confined to a hinge region conserved in all known MHC molecules. This shift causes a narrowing of the two helices flanking the binding site and results in a closure, which is further stabilized by the formation of a critical hydrogen bond between residues ?Q9 and ?N82. Mutagenesis experiments confirmed that replacement of either one of the two residues by alanine renders the protein highly susceptible. Notably, loading enhancement was also observed when the mutated MHC II molecules were expressed on the surface of fibroblast cells. Altogether, structural features underlying the non-receptive state of empty HLA-DR1 identified by theoretical means and experiments revealed highly conserved residues critically involved in the receptiveness of MHC II. The atomic details of rearrangements of the peptide-binding groove upon peptide loss provide insight into structure and dynamics of empty MHC II molecules and may foster rational approaches to interfere with non-receptiveness. Manipulation of peptide loading efficiency for improved peptide vaccination strategies could be one of the applications profiting from the structural knowledge provided by this study.

Dataset Information

Structural characterization of NrnC identifies unifying features of dinucleotidases.

Publications

Structural characterization of NrnC identifies unifying features of dinucleotidases.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets