Structural, molecular, and functional insights into Schlafen proteins

Abstract

Schlafen (SLFN) genes belong to a vertebrate gene family encoding proteins with high sequence homology. However, each SLFN is functionally divergent and differentially expressed in various tissues and species, showing a wide range of expression in cancer and normal cells. SLFNs are involved in various cellular and tissue-specific processes, including DNA replication, proliferation, immune and interferon responses, viral infections, and sensitivity to DNA-targeted anticancer agents. The fundamental molecular characteristics of SLFNs and their structures are beginning to be elucidated. Here, we review recent structural insights into the N-terminal, middle and C-terminal domains (N-, M-, and C-domains, respectively) of human SLFNs and discuss the current understanding of their biological roles. We review the distinct molecular activities of SLFN11, SLFN5, and SLFN12 and the relevance of SLFN11 as a predictive biomarker in oncology.

Fig. 1. The conserved SLFN family gene cluster.

A The locations of SLFN genes in human and mouse chromosomes. The colors indicate orthologous relationships between human and mouse SLFNs (blank: unknown). B Classification of SLFN genes and proteins in human, mouse, and virus. C Phylogenetic tree of SLFN proteins generated by ClustalW2. D Violin plot of human SLFN mRNA expression in the CCLE cancer cell database (CellMinerCDB, discover.nci.nih.gov/cellminercdb). E Correlation of the expression of SLFN genes in human.

Fig. 2. The N-domain of SLFNs.

A Schematic diagram of an SLFN protein. The expanded diagram shows the N-domain of SLFN proteins with the conserved active site. B Sequence alignment of the conserved active site in human, mouse, and virus SLFNs. The sequence alignment was generated using ESPript. C Ribbon diagram of the crystal structure of rSlfn13-N (PDB: 5YD0). BD: bridging domain. D Superimposition of rSlfn13-N, SLFN5-N (PDB: 6RR9), and SLFN12-N (PDB: 7LRE). E The electrostatic surface potentials of rSlfn13-N. The colors indicate electric charge (red: negative and blue: positive). F The electrostatic surface potentials of mSlfn2-N (1-378) (modeled by AlphaFold: AF-Q9Z0I6-F1).

Fig. 3. The M-domain of SLFNs.

A Schematic diagram of the M-domain of SLFN proteins. The ribbon diagram shows the cryo-EM structure of SLFN12-PDE3A (PDB: 7LRD) including the M-domain (green), SWAVDL motif (red), and PIR (PDE3A interacting region; yellow). B The expanded M-domain of SLFN12. C Superimposition of SLFN12-M (PDB: 7LRE), SLFN11-M (AlphaFold: AF-Q7Z7L1-F1), SLFN5-M (AlphaFold: AF-Q08AF3-F1), SLFN12L-M (AlphaFold: AF-Q6IEE8-F1), SLFN13-M (AF-Q68D06-F1), and SLFN14-M (AlphaFold: AF-P0C7P3-F1). D Sequence alignment of the M-domains in human SLFNs. The sequence alignment was generated using ESPript.

Fig. 4. The C-domain of SLFNs.

A Schematic diagram of the C-domain of SLFN proteins. B The ribbon diagram shows the modeled structure of SLFN11 (AlphaFold: AF-Q7Z7L1-F1). The annotations indicate the localization of key elements in SLFN11. C Sequence alignment of the Walker A/B motifs in human SLFNs, mouse Slfn8, and mouse Dna2. The sequence alignment was generated using ESPript. D Schematic diagram of selected proteins targeted by DNA/RNA helicases.

Fig. 5. SLFNs in cancers.

A Correlation of SLFN11 expression with sensitivity to anticancer drugs in the GDSC-MGH-Sanger database (each point is a drug; n = 297) analyzed using CellMinerCDB (https://discover.nci.nih.gov/cellminercdb). B Proposed signaling model for SLFN11 as a replication checkpoint. C Proposed signaling model for SLFN5 as a tumor suppressor and oncogene. D Proposed functional model for SLFN12 with PDE3A activated by estrogen and DNMDP.