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Lu et al. Cell Commun Signal (2021) 19:60 https://doi.org/10.1186/s12964-021-00741-y REVIEW Open Access Types of nuclear localization signals and mechanisms of protein import into the nucleus Juane Lu1, Tao Wu1, Biao Zhang1, Suke Liu1, Wenjun Song1, Jianjun Qiao2,3,4* and Haihua Ruan1* Abstract Nuclear localization signals (NLS) are generally short peptides that act as a signal fragment that mediates the trans- port of proteins from the cytoplasm into the nucleus. This NLS-dependent protein recognition, a process necessary for cargo proteins to pass the nuclear envelope through the nuclear pore complex, is facilitated by members of the importin superfamily. Here, we summarized the types of NLS, focused on the recently reported related proteins containing nuclear localization signals, and briefy summarized some mechanisms that do not depend on nuclear localization signals into the nucleus. Keywords: Nuclear localization signal, Nuclear pore complex, Importin Background a permeability barrier between the cytoplasm and nucle- One of the characteristic features of eukaryotic cells oplasm [5]. Te main structural components of the NPC are membrane-bound functional organelles such as the include the central channel, the cytoplasmic ring moiety nucleus, mitochondria, golgi apparatus, and others, and cytoplasmic flaments, and the nuclear ring moiety which are surrounded by cytoplasm. For cells to function and nuclear basket [6]. Te NPC has eightfold rotational normally, organelle proteins synthesized in the cytoplasm symmetry. Each NPC is connected to the inner and outer must be selectively and efciently transported into their nuclear membranes by symmetrical 8 molecular spoke destination compartments where they can exert their proteins, and the 8 molecular spoke proteins surround physiological functions [1]. Consequently, nucleocyto- each other into a central channel with an outer diameter plasmic transport is an essential process in eukaryotes of 122 nm and an inner diameter of 70 nm [7, 8]. Diverse [2, 3]. Te nucleus has a double membrane called nuclear proteins, such as transcription factors, histones, and cell envelope. In order to allow the exchange of proteins cycle regulators, need to be transported into the nucleus between the nucleus and cytoplasm, proteins must be through the NPC after their synthesis, which necessi- transported efciently through the nuclear pore complex tates the presence of a nuclear localization signal (NLS) (NPC), which penetrates the nuclear envelope [4]. Te on these cargo proteins [9]. Te NLS is recognized by the NPC is a large, multimeric structure that generally acts as corresponding nuclear transporters, which can interact with nucleoporins to help NLS-containing proteins reach the nucleus through NPCs [10]. Due to the complex roles *Correspondence: [email protected]; [email protected] of nuclear proteins, NLS-mediated nuclear transport is a 1 Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, highly regulated process. Here, we briefy review recent Tianjin, China studies that defned NLS sequences in the nuclear import 2 Key Laboratory of Systems Bioengineering, Ministry of Education, of cargo proteins and the mechanisms of protein import Tianjin, China Full list of author information is available at the end of the article mediated by NLS. © The Author(s) 2021. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http:// creat iveco mmons. org/ licen ses/ by/4. 0/. The Creative Commons Public Domain Dedication waiver (http:// creat iveco mmons. org/ publi cdoma in/ zero/1. 0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Lu et al. Cell Commun Signal (2021) 19:60 Page 2 of 10 Overview of nuclear localization signals amino acids, which generally contains 4 or more posi- Unlike proteins bound to the endoplasmic reticulum or tively charged residues, that is, arginine (R) or lysine (K). mitochondria, whose N-terminal targeting signals are Te characteristic motif of MP NLS is usually defned as often cleaved after arrival at their destination organelle, K (K/R) X (K/R), where X can be any residue [17]. For nuclear localization signals remain intact and can be example, the NLS of SV40 large T-antigen is 126PKK- located at almost any part of the protein sequence, indi- KRKV132, with fve consecutive positively charged amino cating the possibility of multiple rounds of nucleocyto- acids (KKKRK). Interestingly, studies have shown that plasmic transport [11]. its reverse sequence has no nuclear transport function A nuclear localization signal (NLS) was frstly identi- [12]. Furthermore, if the third amino acid lysine (K) of fed through the analysis of mutants of simian virus 40 SV40 large T antigen NLS is mutated to threonine (T), its (SV40), whose NLS is composed of seven amino acids, nuclear transport function is also lost [18]. Pro-Lys-Lys-Lys-Arg-Lys-Val (PKKKRKV) [12]. NLS Willis et al. identifed a putative NLS (640PKLKRQ646) sequences were subsequently identifed in numerous in vasopressin-activated calcium-mobilizing protein/cul- other proteins imported into the nucleus. lin5 (VACM-1/CUL5), which is necessary for its nuclear In recent years, NLS were widely used in cancer localization and inhibitory efect on cellular growth. Tis treatment and viral infection prevention [13–15], and sequence starts with a proline (P) and is followed by an researchers paid more attention to identifying novel NLS amino acid sequence containing three basic residues out motifs and the import nucleoporins that recognize and of four (PKLKR) [19]. An analogous NLS, found in the bind them. Here, we categorized NLS according to their 146th-149th amino acids of chemokine receptor CXCR4, residue composition into classical (cNLS), non-classical is composed of Arg-Pro-Arg-Lys (RPRK) [20]. CXCR4 (ncNLS), and other types. showed diferent subcellular distribution in pathological specimens of renal cell carcinoma derived from difer- The classical nuclear localization signals (cNLS) ent sources. In primary renal cell carcinoma, it is mainly As shown in Table 1, the cNLS encompass two catego- distributed in the cell membrane, while in the metastatic ries, termed “monopartite” (MP) and “bipartite” (BP) focus, it is mainly distributed inside the cell and nucleus [16]. MP NLS are a single cluster composed of 4–8 basic [34]. Terefore, nuclear translocation of CXCR4 may be Table 1 Classifcation of nuclear localization signals (partial) Category Source Sequence Transport receptors Classical nuclear localization signals MP NLS VACM-1/CUL5 [19] PKLKRQ Importin α/β1 (cNLS) CXCR4 [20] RPRK VP1 [21] RRARRPRG BP NLS 53BP1 [22] GKRKLITSEEERSPAKRGRKS ING4 [23] KGKKGRTQKEKKAARARSKGKN IER5 [24] RKRCAAGVGGGPAGCPAPGSTPLKKPRR ERK5 [25] RKPVTAQERQREREEKRRRR QERAK- EREKRRQERER Non-classical nuclear localization signals PY-NLS Hrp1 [26] RSGGNHRRNGRG GRG GYNRRNNGYHPY Importin βs (ncNLS) UL79 [27] TLLLRETMNNLGVSDHAVLSRKTPQPY EWS [28] PGKMDKGEHRQERRDRPY Other non-classical PTHrP [29] GKKKKGKPGKRREQRKKKRRT NLS Pho4 [30] SANKVTKNKSNSSPYLNKRKGKPGPDS rpL23a [31] VHSHKKKKIPTSPTFTTPKTLTLRRQPKY- PRKSAPRRNKLDHY Other types of nuclear localization Putative NLS PABPN1 None Importin αs/βs signals Spatial epitope NLS STAT1 None Cryptic NLS FGF2 None Multiple NLS MSX1 [32] RKHKTNRKPR NRRAKAKR NLS-RARα [33] RNKKKK RKVIK Lu et al. Cell Commun Signal (2021) 19:60 Page 3 of 10 one of the important mechanisms leading to invasion and hydrophobic or basic motifs and C-terminal R/K/H(X)2- metastasis of malignant tumors such as renal cell carci- 5PY motifs (where X 2-5 is any sequence of 2–5 residues) noma. Additionally, viral protein1 (VP1) of chicken ane- [27]. Two subclasses, hPY-NLS and bPY-NLS, were mia virus (CAV) was found to contain a functional NLS defned according to their N-terminal motifs. Te hPY- motif necessary for its import into the nucleus. It spans NLS contains φG/A/Sφφ motifs (where φ is a hydro- the amino acids 3RRARRPRG10, which makes it a classi- phobic residue), whereas bPY-NLS is enriched in basic cal MP NLS motif [21]. residues [27]. Collectively, the PY-NLS consensus cor- By contrast, BP NLS are characterized by two clusters responds to [basic/hydrophobic]-Xn- [R/H/K]-(X)2–5-PY of 2–3 positively charged amino acids that are separated [38], where X can be any residue. by a 9–12 amino-acid linker region, which contains sev- Human heterogeneous nuclear ribonucleoprotein A1 eral proline (P) residues [16]. Te consensus sequence (hnRNP A1) is known as hPY-NLS due to its sequence 263 289 can be expressed as R/K(X)10-12KRXK [17]. Notably, in FGNYNNQSSNFGPMKGGNFGGRSSGPY , which BP NLS, the upstream and downstream clusters of amino includes a hydrophobic region (273FGPM276) required
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  • Identification of Proteins Interacting with Dysferlin Using the Tandem Affinity Purification Method

    Identification of Proteins Interacting with Dysferlin Using the Tandem Affinity Purification Method

    The Open Cell Development & Biology Journal, 2008, 1, 17-23 17 Open Access Identification of Proteins Interacting with Dysferlin Using the Tandem Affinity Purification Method Maziar Assadi*,1, Thomas Schindler1, Bernd Muller1, John D. Porter2, Markus A. Ruegg3 and Hanno Langen1 1F. Hoffmann-La Roche, Roche Center for Medical Genomics, Basel, Switzerland 2Case Western Reserve University, Department of Neurology, Cleveland, USA 3University of Basel, Biozentrum, Basel, Switzerland Abstract: Mutations of DYSF, the gene encoding dysferlin, cause two types of muscular dystrophies: limb-girdle muscu- lar dystrophy type 2B and Miyoshi myopathy. Recent work suggests a role of dysferlin in membrane repair and demon- strates that defective membrane repair is a novel mechanism of muscle degeneration. We used the tandem affinity purifi- cation method for the purification of proteins interacting with dysferlin. Three interacting partners were identified by this method (striatin, adaptin alpha, utrophin) and were confirmed by co-immunoprecipitations. All three proteins play a role in vesicle trafficking. Knowing the interacting partners of dysferlin will help to understand how muscle cells repair tears in the sarcolemma and will give a deeper insight into this very important cell function. At the same time the identified proteins could serve as potential candidates for other muscular dystrophies and muscle-related diseases with unknown ae- tiology. INTRODUCTION this machinery. These proteins could serve as potential can- didate for other muscular dystrophies and muscle-diseases Dysferlin is a member of a mammalian gene family shar- with unknown aetiology. Therefore, we attempted to identify ing homology with the Caenorhabditis elegans spermato- the interacting partners of dysferlin and used the tandem genesis factor fer-1 gene, which mediates vesicle fusion to affinity purification (TAP) method for this purpose.