Solid-state photochemical reactions of olefinic compounds have been demonstrated to represent powerful access to organic cyclic molecules with specific configurations. However, the precise control of ...the stereochemistry in these reactions remains challenging owing to complex and fleeting configuration transformations. Herein, we report a unique approach to control the regiospecific configurations of C = C groups and the intermediates by varying temperatures in multiple-step thermal/photoinduced reactions, thus successfully realizing reversible ring closing/opening changes using a single-crystal coordination polymer platform. All stereochemical transitions are observed by in situ single-crystal X-ray diffraction, powder X-ray diffraction and infrared spectroscopy. Density functional theory calculations allow us to rationalize the mechanism of the synergistic thermal/photoinduced transformations. This approach can be generalized to the analysis of the possible configuration transformations of functional groups and intermediates and unravel the detailed mechanism for any inorganic, organic and macromolecular reactions susceptible to incorporation into single-crystal coordination polymer platforms.
Activation-induced cytidine deaminase (AID)-single-strand (ss)DNA binding mode determines both microscale WRC preference and mesoscale complementarity determining region (CDR) preference; ...apolipoprotein B editing complex (APOBEC3)A uses a distinct binding mode and shows different DNA sequence preferences.The flexible ssDNA are AID-favored substrates in vitro and in vivo.Chromatin loop extrusion, superenhancer, and transcription stalling create a hierarchical order for AID deamination in chromatin loop domains.5-Hydroxymethylcytosine binding, ES cell specific (HMCES) is the factor that prevents AID lesions from processing into double-strand breaks in somatic hypermutation (SHM).Aberrant SHM directly regulates oncogene expression in lymphomagenesis, and promotes cell growth for a fraction of B cells expressing autoantibodies.A safer base editor could be designed based on the knowledge of AID-lesion repair.
Activation-induced cytidine deaminase (AID) initiates somatic hypermutation (SHM) by introducing base substitutions into antibody genes, a process enabling antibody affinity maturation in immune response. How a mutator is tamed to precisely and safely generate programmed DNA lesions in a physiological process remains unsettled, as its dysregulation drives lymphomagenesis. Recent research has revealed several hidden features of AID-initiated mutagenesis: preferential activity on flexible DNA substrates, restrained activity within chromatin loop domains, unique DNA repair factors to differentially decode AID-caused lesions, and diverse consequences of aberrant deamination. Here, we depict the multifaceted regulation of AID activity with a focus on emerging concepts/factors and discuss their implications for the design of base editors (BEs) that install somatic mutations to correct deleterious genomic variants.
Activation-induced cytidine deaminase (AID) initiates somatic hypermutation (SHM) by introducing base substitutions into antibody genes, a process enabling antibody affinity maturation in immune response. How a mutator is tamed to precisely and safely generate programmed DNA lesions in a physiological process remains unsettled, as its dysregulation drives lymphomagenesis. Recent research has revealed several hidden features of AID-initiated mutagenesis: preferential activity on flexible DNA substrates, restrained activity within chromatin loop domains, unique DNA repair factors to differentially decode AID-caused lesions, and diverse consequences of aberrant deamination. Here, we depict the multifaceted regulation of AID activity with a focus on emerging concepts/factors and discuss their implications for the design of base editors (BEs) that install somatic mutations to correct deleterious genomic variants.
To obtain a pure product without the isomer byproducts is a goal that many chemists are pursuing. As one kind of very important synthesis method, the photochemical reaction is simple and ...straightforward yet low-selective. In this work, a coordination interaction-based oriented synthesis strategy has been proposed to realize the precise stereochemical control of the isomeric cyclic compounds in the photocycloaddition reaction. Through fixing the reactants via coordination interactions, the arrangements and configurations of the reactants can be adjusted, thereby successfully producing all of the related photocycloaddition products without isomer byproducts for the first time. This work not only provides a new route to synthesize the pure cyclic compounds but also expands the application of the photocycloaddition reaction.
The accurate taxonomic concept of the fungal
Chaetomium
species has been a hard work due to morphological similarity. Chemotaxonomy based on secondary metabolites is a powerful tool for taxonomical ...purposes, which could be used as an auxiliary reference to solve the problems encountered in the classification of
Chaetomium
. Among secondary metabolites produced by
Chaetomium
, cytochalasans and azaphilones exhibited a pattern of distribution and frequency of occurrence that establish them as chemotaxonomic markers for the
Chaetomium
species. This review attempted to elucidate the composition of the
Chaetomium
species and its relationship with classical taxonomy by summarizing the pattern of cytochalasans and azaphilones distribution and biosynthesis in the
Chaetomium
species.
Key points
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Secondary metabolites from the genus Chaetomium are summarized.
•
Cytochalasans and azaphilones could be characteristic metabolites of the Chaetomium species.
•
Cytochalasans and azaphilones could be used to analyze for taxonomical purposes.
Graphical abstract
Activation-induced cytidine deaminase (AID) initiates both class switch recombination (CSR) and somatic hypermutation (SHM) in antibody diversification. Mechanisms of AID targeting and catalysis ...remain elusive despite its critical immunological roles and off-target effects in tumorigenesis. Here, we produced active human AID and revealed its preferred recognition and deamination of structured substrates. G-quadruplex (G4)-containing substrates mimicking the mammalian immunoglobulin switch regions are particularly good AID substrates in vitro. By solving crystal structures of maltose binding protein (MBP)-fused AID alone and in complex with deoxycytidine monophosphate, we surprisingly identify a bifurcated substrate-binding surface that explains structured substrate recognition by capturing two adjacent single-stranded overhangs simultaneously. Moreover, G4 substrates induce cooperative AID oligomerization. Structure-based mutations that disrupt bifurcated substrate recognition or oligomerization both compromise CSR in splenic B cells. Collectively, our data implicate intrinsic preference of AID for structured substrates and uncover the importance of G4 recognition and oligomerization of AID in CSR.
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•Structured substrates, such as G4 substrates, are preferred AID targets in vitro•A bifurcated substrate-binding surface supports structured-substrate recognition•G4 substrates induce AID oligomerization upon binding•Disrupting structured-substrate recognition or AID oligomerization compromises CSR
Qiao et al. demonstrated that structured substrates, like G4 and branched DNA, are preferred AID targets in vitro. A bifurcated substrate-binding surface in AID structure supports structured-substrate recognition. G4 substrates mimicking the Ig S regions also induce cooperative AID oligomerization. Disrupting structured-substrate recognition or AID oligomerization both compromise CSR.
In activated B cells, activation‐induced cytidine deaminase (AID) generates programmed DNA lesions required for antibody class switch recombination (CSR), which may also threaten genome integrity. ...AID dynamically shuttles between cytoplasm and nucleus, and the majority stays in the cytoplasm due to active nuclear export mediated by its C‐terminal peptide. In immunodeficient‐patient cells expressing mutant AID lacking its C‐terminus, a catalytically active AID‐delC protein accumulates in the nucleus but nevertheless fails to support CSR. To resolve this apparent paradox, we dissected the function of AID‐delC proteins in the CSR process and found that they cannot efficiently target antibody genes. We demonstrate that AID‐delC proteins form condensates both in vivo and in vitro, dependent on its N‐terminus and on a surface arginine‐rich patch. Co‐expression of AID‐delC and wild‐type AID leads to an unbalanced nuclear AID‐delC/AID ratio, with AID‐delC proteins able to trap wild‐type AID in condensates, resulting in a dominant‐negative phenotype that could contribute to immunodeficiency. The co‐condensation model of mutant and wild‐type proteins could be an alternative explanation for the dominant‐negative effect in genetic disorders.
Synopsis
Immunodeficiency‐associated activation‐induced deaminase (AID) variants lacking the C‐terminus behave as dominant‐negative in antibody diversification. This study reveals co‐condensation as a basis of this dominant‐negative effect, with mutant AID proteins forming condensates and trapping wild‐type AID from its substrates.
The AID C‐terminus is required for its recruitment to genomic antibody switch regions
C‐terminal‐deleted AID protein forms condensates in vitro and in vivo
AID condensation causes a faulty distribution of deaminase activity
C‐terminal‐deleted AID co‐condensates with wild‐type protein, resulting in the dominant‐negative effect
The dominant‐negative effect of immunodeficiency‐associated activation‐induced deaminase variants lacking the C‐terminus can be explained by its trapping of wild‐type AID away from antibody switch regions.
Chromosomal translocations involving antigen receptor loci are common in lymphoid malignancies. Translocations require DNA double-strand breaks (DSBs) at two chromosomal sites, their physical ...juxtaposition, and their fusion by end-joining. Ability of lymphocytes to generate diverse repertoires of antigen receptors and effector antibodies derives from programmed genomic alterations that produce DSBs. We discuss these lymphocyte-specific processes, with a focus on mechanisms that provide requisite DSB target specificity and mechanisms that suppress DSB translocation. We also discuss recent work that provides new insights into DSB repair pathways and the influences of three-dimensional genome organization on physiological processes and cancer genomes.
Programmed DNA recombination in mammalian cells occurs predominantly in a directional manner. While random DNA breaks are typically repaired both by deletion and by inversion at approximately equal ...proportions, V(D)J and class switch recombination (CSR) of immunoglobulin heavy chain gene overwhelmingly delete intervening sequences to yield productive rearrangement. What factors channel chromatin breaks to deletional CSR in lymphocytes is unknown. Integrating CRISPR knockout and chemical perturbation screening we here identify the Snf2-family helicase-like ERCC6L2 as one such factor. We show that ERCC6L2 promotes double-strand break end-joining and facilitates optimal CSR in mice. At the cellular levels, ERCC6L2 rapidly engages in DNA repair through its C-terminal domains. Mechanistically, ERCC6L2 interacts with other end-joining factors and plays a functionally redundant role with the XLF end-joining factor in V(D)J recombination. Strikingly, ERCC6L2 controls orientation-specific joining of broken ends during CSR, which relies on its helicase activity. Thus, ERCC6L2 facilitates programmed recombination through directional repair of distant breaks.
Growth signals, such as extracellular nutrients and growth factors, have substantial effects on genome integrity; however, the direct underlying link remains unclear. Here, we show that the ...mechanistic target of rapamycin (mTOR)-ribosomal S6 kinase (S6K) pathway, a central regulator of growth signalling, phosphorylates RNF168 at Ser60 to inhibit its E3 ligase activity, accelerate its proteolysis and impair its function in the DNA damage response, leading to accumulated unrepaired DNA and genome instability. Moreover, loss of the tumour suppressor liver kinase B1 (LKB1; also known as STK11) hyperactivates mTOR complex 1 (mTORC1)-S6K signalling and decreases RNF168 expression, resulting in defects in the DNA damage response. Expression of a phospho-deficient RNF168-S60A mutant rescues the DNA damage repair defects and suppresses tumorigenesis caused by Lkb1 loss. These results reveal an important function of mTORC1-S6K signalling in the DNA damage response and suggest a general mechanism that connects cell growth signalling to genome stability control.
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