Developing high-efficiency base editors by combining optimized synergistic core components with new types of nuclear localization signal peptide

The clustered regularly interspaced short palindromic repeats(CRISPR)–CRISPR-associated protein(Cas) system has been widely used for genome editing. In this system, the cytosine base editor(CBE) and adenine base editor(ABE) allow generating precise and irreversible base mutations in a programmable manner and have been used in many different types of cells and organisms. However, their applications are limited by low editing efficiency at certain genomic target sites or at specific target cytosine(C) or adenine(A) residues. Using a strategy of combining optimized synergistic core components, we developed a new multiplex super-assembled ABE(sABE) in rice that showed higher base-editing efficiency than previously developed ABEs. We also designed a new type of nuclear localization signal(NLS) comprising a FLAG epitope tag with four copies of a codon-optimized NLS(F4NLS^(r2)) to generate another ABE named F4NLS-sABE. This new NLS increased editing efficiency or edited additional A at several target sites. A new multiplex super-assembled CBE(sCBE) and F4NLS^(r2) involved F4NLS-sCBE were also created using the same strategy. F4NLS-sCBE was proven to be much more efficient than sCBE in rice. These optimized base editors will serve as powerful genome-editing tools for basic research or molecular breeding in rice and will provide a reference for the development of superior editing tools for other plants or animals.

Presence of a long nuclear-localization signal sequence in homeodomain transcription factor Nkx 1.2

Homeodomains,a 60-amino acid sequence encoded by 180 nucleotides,are highly conserved DNA-binding motifs that are present in a variety of transcription factors in species ranging from yeast to humans.The NKX proteins belong to the homeodomain(HD)-containing transcription factor family.They play vital roles in the regulation of morphogenesis.NKX1-2 is one member of the NKX subfamily.At present,information about its nuclear localization signal(NLS)sequence is limited.We studied the NLS sequence of zebrafish Nkx1.2 by introducing sequence changes such as deletion,mutation,and truncation,and identified an NLS motif(QNRRTKWKKQ)that is localized at the C-terminus of the homeodomain.Moreover,the deletion of two amino acid residues(RR)in this NLS motif prevents Nkx1.2 from entering the nucleus,indicating that the two amino acids are essential for Nkx1.2 nuclear localization.However,the NLS motif alone is unable to target cytoplasmic protein glutathione S-transferase(GST)to the nucleus.An intact homeodomain is necessary for mediating the complete nuclear transport of cytoplasmic protein.Unlike most nuclear import proteins with short NLS sequences,a long NLS is present in zebrafish Nkx1.2.We also demonstrated that the sequences of homeodomain of NKX1.2 are well conserved among different species.This study is informative to verify the function of the NKX1.2 protein.

Predicting the Nuclear Localization Signals of 107 Types of HPV L1 Proteins by Bioinformatic Analysis

In this study, 107 types of human papillomavirus （HPV） L1 protein sequences were obtained from available databases, and the nuclear localization signals （NLSs） of these HPV L1 proteins were analyzed and predicted by bioinformatic analysis. Out of the 107 types, the NLSs of 39 types were predicted by PredictNLS software （35 types of bipartite NLSs and 4 types of monopartite NLSs）. The NLSs of the remaining HPV types were predicted according to the characteristics and the homology of the already predicted NLSs as well as the general rule of NLSs. According to the result, the NLSs of 107 types of HPV L1 proteins were classified into 15 categories. The different types of HPV L1 proteins in the same NLS category could share the similar or the same nucleocytoplasmic transport pathway. They might be used as the same target to prevent and treat different types of HPV infection. The results also showed that bioinformatic technology could be used to analyze and predict NLSs of proteins.

A Dual Mechanism Controls Nuclear Localization in the Atypical Basic-Helix-Loop-Helix Protein PAR1 of Arabidopsis thaliana

PAR1 is an atypical basic-helix-loop-helix （bHLH） protein that negatively regulates the shade avoidance syndrome in Arabidopsis thaliana acting as a transcriptional cofactor. Consistently with this function, PAR1 has to be in the nucleus to display biological activity. Previous structure-function analyses revealed that the N-terminal region of PAR1 drives the protein to the nucleus. However, truncated forms of PAR1 lacking this region still display biological activity, implying that PAR1 has additional mechanisms to localize into the nucleus. In this work, we compared the primary structure of PAR1 and various related and unrelated plant bHLH proteins, which led us to suggest that PAR1 contains a non-canonical nuclear localization signal （NLS） in the N-terminal region. By overexpressing truncated and mutated derivatives of PAR1, we have also investigated the importance of other regions of PAR1, such as the acidic and the extended HLH dimerization domains, for its nuclear localization. We found that, in the absence of the N-terminal region, a functional HLH domain is required for nuclear localization. Our results suggest the existence of a dual mechanism for PAR1 nuclear localization： （1） one mediated by the N-terminal non-consensus NLS and （2） a second one that involves interaction with other proteins via the dimerization domain,

Identification of karyopherin-alpha 2 as an Oct4 associated protein

The POU domain transcription factor Oct4 is a master regulator in maintaining self-renewal and pluripotency of embryonic stem （ES） cells. To further explore the functional network of Oct4, the yeast two-hybrid system was used to search for Oct4 interacting proteins. PH domain （containing POU domain and homeodomain） of human OCT4 was used as a bait. From the human testis cDNA library, we identified a strong interaction between OCT4 and karyopberin-alpha 2 （KPNA-2）. KPNA2 is involved in active nuclear import of proteins. This finding was confirmed by glutathione S-transferase pull-down and co-immunoprecipitation assays. The interaction between OCT4 and KPNA-2 was further mapped to multiple regions of the two proteins. In addition, we studied nuclear localization signal （NLS） of mouse Oct4 and demonstrated that it is essential for Oct4 nuclear localization. Thus, our data suggest that Oct4 nuclear localization may be mediated by its interaction with KPNA-2.

A novel hierarchical targeting and controllable smart nanoparticles for enhanced in situ nuclear photodynamic therapy

Photodynamic therapy(PDT)is a promising and non-invasive treatment for various cancers.Although nuclear PDT has considerable therapeutic prospects,it is still hindered by the non-specific recognition of tumor tissues or the degradation of nuclear targeting cationic groups by enzymes in the blood.Herein,a hierarchical targeted and controlled release strategy is proposed by using folate-modified poly-β-cyclodextrin(poly-β-CD)as a nano-carrier for loading nuclear localization signals(NLSs)-conjugated photosensitizer PAP(PAP=pyropheophorbide a-PAAKRVKLD).Excitingly,the obtained FA-CD@PAP(FA=folic acid)and nanoparticles(NPs)can specifically recognize tumor cells overexpressing folate receptors(FR)to remarkedly enhance the intracellular accumulation.Furthermore,the encapsulated PAP can be released under acidic conditions to realize precise nuclear localization.The reactive oxygen species(ROS)generated by the intranuclear-accumulated PAP upon irradiation can oxidize and destroy DNA chains or DNA repair enzymes instantaneously,which can directly induce cell death.As a result,FA-CD@PAP NPs exhibit excellent tumor regression and negligible side effects.This work provides an intelligent nuclear-targeted delivery strategy for in situ nuclear PDT with extremely prominent efficacy and high biological safety.

The SNW Domain of SKIP Is Required for Its Integration into the Spliceosome and Its Interaction with the Pall Complex in Arabidopsis

SKIP is a conserved protein from yeasts to plants and humans. In plant cells, SKIP is a bifunctional regulator that works in the nucleus as a splicing factor by integrating into the spliceosome and as a transcriptional activator by interacting with the Pall complex. In this study, we identified two nuclear localization signals in SKIP and confirmed that each is sufficient to target SKIP to the nucleus. The SNW domain of SKIP is required for both its function as a splicing factor by promoting integration into the spliceosome in response to stress, and its function as a transcriptional activator by controlling its interaction with the Pall complex to participate in flowering. Truncated proteins that included the SNW domain and the N- or C-terminus of SKIP were still able to carry out the functions of the full-length protein in gene splicing and transcriptional activation in Arabidopsis. In addition, we found that SKIP undergoes 26S proteasome-mediated degrada- tion, and that the C-terminus of SKIP is required to maintain the stability of the protein in plant cells. Together, our findings demonstrate the structural domain organization of SKIP and reveal the core domains and motifs underlying SKIP function in plants.

Role of Intracellular Distribution of Feline and Bovine SAMHD1 Proteins in Lentiviral Restriction

Human SAMHD1(h SAM)restricts lentiviruses at the reverse transcription step through its d NTP triphosphohydrolase(d NTPase)activity.Besides humans,several mammalian species such as cats and cows that carry their own lentiviruses also express SAMHD1.However,the intracellular distribution of feline and bovine SAMHD1(f SAM and b SAM)and its significance in their lentiviral restriction function is not known.Here,we demonstrated that f SAM and b SAM were both predominantly localized to the nucleus and nuclear localization signal(11KRPR14)-deleted f SAM and b SAM relocalized to the cytoplasm.Both cytoplasmic f SAM and b SAM retained the antiviral function against different lentiviruses and cytoplasmic f SAM could restrict Vpx-encoding SIV and HIV-2 more efficiently than its wild-type(WT)protein as cytoplasmic h SAM.Further investigation revealed that cytoplasmic f SAM was resistant to Vpx-induced degradation like cytoplasmic h SAM,while cytoplasmic b SAM was not,but they all demonstrated the same in vitro d NTPase activity and all could interact with Vpx as their WT proteins,indicating that cytoplasmic h SAM and f SAM can suppress more SIV and HIV-2 by being less sensitive to Vpx-mediated degradation.Our results suggested that f SAM-and b SAM-mediated lentiviral restriction does not require their nuclear localization and that f SAM shares more common features with h SAM.These findings may provide insights for the establishment of alternative animal models to study SAMHD1 in vivo.