A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice, Wiki and Databases.

Abstract

In recent years, a vast number of novel antiphage defense mechanisms were uncovered. To facilitate the exploration of mechanistic, ecological, and evolutionary aspects related to antiphage defense systems, we released DefenseFinder in 2021 (Tesson et al., 2022). DefenseFinder is a bioinformatic program designed for the systematic identification of all known antiphage defense mechanisms. The initial release of DefenseFinder v1.0.0 included 60 systems. Over the past three years, the number of antiphage systems incorporated into DefenseFinder has grown to 152. The increasing number of known systems makes it a challenge to enter the field and makes the interpretation of detections of antiphage systems difficult. Moreover, the rapid development of sequence-based predictions of structures offers novel possibilities of analysis and should be easily available. To overcome these challenges, we present a hub of resources on defense systems including 1) a search tool (DefenseFinder as a web service) 2) a knowledge base, and 3) precomputed databases (results of DefenseFinder ran on RefSeq database, predicted structure database computed with Alpha​F​old). These pages can be freely accessed for users as a starting point on their journey to better understand a given system. We anticipate that these resources will foster the use of bioinformatics in the study of antiphage systems and will serve the community of researchers who study antiphage systems. This resource is available at: https://defensefinder.mdmlab.fr.

Hachiman is a genome integrity sensor

“…This is also true for prokaryotic immune systems. Of the ∽150 defense systems cataloged in DefenseFinder 17 , 18 contain an SF1/SF2 helicase, comprising nearly 20% of non-restriction-modification (RM) defense loci identified in RefSeq ( Fig. 1A ) 19 .…”

“…To focus our analysis on the helicase core domain, we manually curated the helicase core domain of defense-associated helicases through structural alignment followed by sequence alignment. First, a predicted AlphaFold2 structure of each defense-associated helicase was aligned to the core helicase domain of HamB (PDB ID: 8VXA, this work, residues 286-472, 500-731) 17,66,67 within the core helicase domain were inferred. Next, for each helicase type, representative helicases were aligned to the corresponding annotated reference using MUSCLE (default parameters), core helicase annotation extracted and insertions removed in Geneious Prime v2023.2.1 68,69 To build the helicase tree, sequences were concatenated with a curated set of SF1/SF2 core helicase domains 12 , aligned using ClustalOmega (default parameters), phylogenized using IQ-TREE (-bb 1000, -m MFP (optimal model: LG+R8)), bootstraps inferred using UFBoot2 and visualized using iTOL [70][71][72][73] .…”

“…Proteins chosen for phylogenetic analysis were from DefenseFinder RefSeq db with a RefSeq Protein ID 16,17 . Proteins from non-Restriction-Modification (RM) defense systems encoding a SF1/SF2 helicase domain were further selected for phylogenetic comparison: AbiR (AbiRc), Azaca (ZacC), BREX (BrxHI, BrxHII), DISARM (DrmA, DrmD), Dpd (DpdE, DpdF, DpdJ), Druantia (DruE), Gabija (GajB), Gao_RL (RL), Hachiman (HamB), Hhe (HheA), Hna (Hna), Mokosh (MkoA, MkoC), Nhi (Nhi), PsyrTA (PsyrT), Rst Helicase+DUF2290 (Helicase), Shango (SngC), Type I CRISPR-Cas (Cas3), Type IV CRISPR-Cas (Csf4/DinG), and Zorya (ZorD).…”

“…1B, see Methods). We confidently assigned 20 of the 25 helicases to an established helicase subfamily, spanning 7 subfamilies: SF1_UvrD (GajB, Nhi, Rst_DUF2290 Helicase), SF1_Upf1 (Hhe, MkoA, MkoC), SF2_Cas3 (Cas3), SF2_Rad3 (Csf4, Hna), SF2_RecQ (DpdF, 17 . (B) Phylogenetic tree of core helicase domains of 329 helicases from defense systems from (A) and representative SF1/SF2 helicases 12 .…”

“… (A) Overview of SF1/SF2 helicase-containing phage defense systems found in RefSeq genomes in the DefenseFinder database 17 . (B) Phylogenetic tree of core helicase domains of 329 helicases from defense systems from (A) and representative SF1/SF2 helicases 12 .…”