cells Review DEAD-Box RNA Helicases in Cell Cycle Control and Clinical Therapy Lu Zhang 1,2 and Xiaogang Li 2,3,* 1 Department of Nephrology, Renmin Hospital of Wuhan University, Wuhan 430060, China; [email protected] 2 Department of Internal Medicine, Mayo Clinic, 200 1st Street, SW, Rochester, MN 55905, USA 3 Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 1st Street, SW, Rochester, MN 55905, USA * Correspondence: [email protected]; Tel.: +1-507-266-0110 Abstract: Cell cycle is regulated through numerous signaling pathways that determine whether cells will proliferate, remain quiescent, arrest, or undergo apoptosis. Abnormal cell cycle regula- tion has been linked to many diseases. Thus, there is an urgent need to understand the diverse molecular mechanisms of how the cell cycle is controlled. RNA helicases constitute a large family of proteins with functions in all aspects of RNA metabolism, including unwinding or annealing of RNA molecules to regulate pre-mRNA, rRNA and miRNA processing, clamping protein complexes on RNA, or remodeling ribonucleoprotein complexes, to regulate gene expression. RNA helicases also regulate the activity of specific proteins through direct interaction. Abnormal expression of RNA helicases has been associated with different diseases, including cancer, neurological disorders, aging, and autosomal dominant polycystic kidney disease (ADPKD) via regulation of a diverse range of cellular processes such as cell proliferation, cell cycle arrest, and apoptosis. Recent studies showed that RNA helicases participate in the regulation of the cell cycle progression at each cell cycle phase, including G1-S transition, S phase, G2-M transition, mitosis, and cytokinesis. In this review, we Citation: Zhang, L.; Li, X. DEAD-Box RNA Helicases in Cell Cycle Control discuss the essential roles and mechanisms of RNA helicases in the regulation of the cell cycle at and Clinical Therapy. Cells 2021, 10, different phases. For that, RNA helicases provide a rich source of targets for the development of 1540. https://doi.org/10.3390/ therapeutic or prophylactic drugs. We also discuss the different targeting strategies against RNA cells10061540 helicases, the different types of compounds explored, the proposed inhibitory mechanisms of the compounds on specific RNA helicases, and the therapeutic potential of these compounds in the Academic Editors: Ritva Tikkanen treatment of various disorders. and Alexander E. Kalyuzhny Keywords: DEAD-box RNA helicases; cell cycle; treatment; DDX5; DDX3 Received: 10 May 2021 Accepted: 15 June 2021 Published: 18 June 2021 1. Introduction Publisher’s Note: MDPI stays neutral 1.1. Cell Cycle with regard to jurisdictional claims in published maps and institutional affil- The cell cycle is a series of events that occur in the interphase and mitotic phase iations. (M-phase) [1,2]. The interphase is the longest phase of the cell cycle in which the genetic material gets duplicated and the cell prepares for division. The interphase includes three sub-phases: (1) G1-phase; the first-gap phase. In the G1-phase, cells grow in size, synthesize cell organelles and other proteins, and accumulate sufficient energy to prepare for cell division. (2) S-phase; the synthesis and DNA-replication phase. The centrosome and DNA Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. are duplicated and give rise to the mitotic spindle during this phase. (3) G2-phase; the This article is an open access article second gap phase. In the G2 phase, cells accumulate energy and grow further in size. distributed under the terms and Following the interphase is a period called the mitotic phase (M-phase). The M-phase conditions of the Creative Commons includes two different critical processes: mitosis and cytokinesis. Mitosis consists of four Attribution (CC BY) license (https:// sub-phases: prophase, metaphase, anaphase, and telophase. The cell divides the nucleus creativecommons.org/licenses/by/ and a complete set of chromosomes into two daughter cells during mitosis. The cytoplasm 4.0/). splits and forms two independent cells in the process of cytokinesis [3,4] (Figure1). The cell Cells 2021, 10, 1540. https://doi.org/10.3390/cells10061540 https://www.mdpi.com/journal/cells Cells 2021, 10, x FOR PEER REVIEW 2 of 20 splits and forms two independent cells in the process of cytokinesis [3,4] (Figure 1). The Cells 2021, 10, 1540 cell cycle is regulated by a series of cell cycle regulatory proteins.2 of 20 Cyclins and cyclin-de- pendent kinases (CDKs) families are key regulators of cell cycle progression [5]. At least nine CDKs are identified in animal cells, in which CDK1, CDK2, CDK3, and CDK4 are cycle is regulated by a series of cell cycle regulatory proteins. Cyclins and cyclin-dependent kinasesinvolved (CDKs) in families the aredirect key regulators regulat ofion cell cycleof the progression cell cycle [5]. At [6] least. In nine general, CDKs CDKs that are active at areeach identified stage in animalpartner cells, with in which cyclins CDK1, CDK2,to regulate CDK3, and cell CDK4 cycle are involvedprogression. in CDK1 drives the cell the direct regulation of the cell cycle [6]. In general, CDKs that are active at each stage partnercycle with of cyclinsG2 and to regulate M-phase cell cycle with progression. its partn CDK1ers drives, cyclin the cell A2 cycle and of G2cyclin and B1. CDK2 drives the cell M-phasecycle withof G1, its partners, S, and cyclin G2 A2 phases and cyclin with B1. CDK2 its drivespartners the cell, cyclin cycle of G1,A, S, cyclin and D, and cyclin E. CDK3 G2 phases with its partners, cyclin A, cyclin D, and cyclin E. CDK3 drives the cell cycle of G0drives phase with the its cell partner, cycle cyclin of C.G0 CDK4 phase andCDK6 with drive its partner the cell cycle, cyclin of G1 phase, C. CDK4 with and CDK6 drive the cell itscycle partners, of cyclinG1 phase D (D1, D2,, with and D3)its andpartners cyclin E, (Figure cyclin1). D (D1, D2, and D3) and cyclin E (Figure 1). FigureFigure 1. Schematic 1. Schematic representation representation of the cell cycle. of The the cell cell cycle cycle. is divided The into cell interphase cycle is (G1, divided into interphase (G1, S, S,G2) G2) andand mitotic mitotic phases. phase Nondividings. Nondividing cells are in G0. cells Cell are cycle in progression G0. Cell is controlledcycle progression by is controlled by cy- cyclin/cyclin-dependent kinase (CDK) complexes in specific cell cycle phases. clin/cyclin-dependent kinase (CDK) complexes in specific cell cycle phases. During the cell cycle, there are three checkpoints that occur at the end of G1 and the transition of G2/M, and in metaphase. The G1 checkpoint blocks the entry of the cell cycle into the SDuring phase if a the cell doescell not cycle, fulfill allthere the conditions, are three which checkpoints lets the cell try that to solve occur the at the end of G1 and the conditions,transition or lets of the G2/M, cell enter and into in the metaphase. G0 phase. The GThe2 checkpoint G1 checkpoint bars the entry blocks of the the entry of the cell cycle cell cycle into the mitotic phase if certain conditions are not met, which ensures that all of theinto genetic the material S phase has beenif a replicatedcell does and not is not fulfill damaged. all Athe damaged conditions DNA will, which halt lets the cell try to solve thethe cell condition cycle to let thes, damagedor lets the DNA cell be repaired. enter into The M the checkpoint, G0 phase also named. The asG2 the checkpoint bars the entry of spindlethe cell checkpoint, cycle isinto a point the close mitotic to the end phase of the metaphase if certain stage conditions to make sure whetherare not met, which ensures that each pair of sister chromatids is correctly anchored to the two spindle microtubules—if not,all the of cycle the willgenetic be halted. material Recent studieshas been suggest replicated that RNA helicases and is are not involved damaged. in A damaged DNA will thesehalt processes. the cell cycle to let the damaged DNA be repaired. The M checkpoint, also named as the spindle checkpoint, is a point close to the end of the metaphase stage to make sure whether each pair of sister chromatids is correctly anchored to the two spindle microtu- bules—if not, the cycle will be halted. Recent studies suggest that RNA helicases are in- volved in these processes. 1.2. RNA Helicases RNA helicases are ubiquitous, highly conserved enzymes that involve in nearly all aspects of RNA metabolism. RNA helicases use ATP to bind or remodel RNA, RNA sec- ondary structure or ribonucleoprotein (RNP) complexes that are associated with RNA transcription, degradation, translation initiation, mRNA splicing, and ribosome biogene- sis [7–9]. RNA helicases are grouped into various superfamilies dependent on the contents of conserved motifs. Most of RNA helicases relate to the superfamily 2 (SF2) of helicases Cells 2021, 10, 1540 3 of 20 1.2. RNA Helicases Cells 2021, 10, x FOR PEER REVIEW 3 of 20 RNA helicases are ubiquitous, highly conserved enzymes that involve in nearly all aspects of RNA metabolism. RNA helicases use ATP to bind or remodel RNA, RNA secondary structure or ribonucleoprotein (RNP) complexes that are associated with RNA transcription,comprising degradation, eleven subfamilies, translation five initiation, of which mRNA are splicing, termed and the ribosome DExH/D biogene- helicases (DEAD- sis [7–9]. RNA helicases are grouped into various superfamilies dependent on the contents box, RIG-I-like DExH, SKI2-like DExH, viral DExH, and DEAH/RHA) with a conserved of conserved motifs. Most of RNA helicases relate to the superfamily 2 (SF2) of helicases comprisingmotif (Asp eleven-Glu subfamilies,-Ala-Asp/His) five of [10] which.