ICEberg 2.0: an updated database of bacterial integrative and conjugative elements

Abstract

ICEberg 2.0 (http://db-mml.sjtu.edu.cn/ICEberg/) is an updated database that provides comprehensive information about bacterial integrative and conjugative elements (ICEs). Compared with the previous version, three major improvements were made. First, with the aid of text mining and manual curation, it now recorded the details of 1032 ICEs, including 270 with experimental supports and 762 from bioinformatics prediction. Second, as increasing evidence has shown that ICEs frequently mobilize the so-called ‘hitchhikers’, such as integrative and mobilizable elements (IMEs) and cis-mobilizable elements (CIMEs), 83 known transfer interactions between 49 IMEs and 7 CIMEs with 19 ICEs taken from the literature were included and illustrated with visually intuitive directed graphs. An expanded collection of 260 chromosome-borne IMEs and 235 CIMEs was also added. At last, ICEberg 2.0 provides an online tool ICEfinder to predict ICEs or IMEs in bacterial genome sequences. It combines a similarity search for the integrase, relaxase and/or type IV secretion system and the co-localization of these corresponding homologous genes. With the recent updates, ICEberg 2.0 might provide better support for understanding the biological traits of ICEs, especially as their interaction with cognate mobilizable elements may further promote horizontal gene flow.

New candidates for regulated gene integrity revealed through precise mapping of integrative genetic elements

“…Table 1 (137 archaeal, 2031 bacterial) that were used for Islander (43), 1010 temperate viruses listed in Supp. Table 2 (the bacterial or archaeal viral isolates from GenBank that we found to encode a Y-Int or S-Int), 109 experimentally-validated ICEs (44), and sets of 3266 GInegative segments (13.8 kbp average) and 1845 GI-positive segments (11.6 kbp average) from 104 genomes, and 80 "gold standard" GI calls (38.3 kbp average) from the literature for 6 genomes (45). The software developed below, run on the 2168 genomes, yielded 6415 (TIGER/Islander mode), 4762 (TIGER-only mode) and 3191 (Islander-only mode) IGEs.…”

“…Two heuristics were devised for phage calling: Phage1 (query matches at least one virion and one non-virion phage HMM), or Phage2 (query matches ≥1 phage HMM from one of these categories). ICE calling employed a set of 47 HMMs for proteins functioning in ICE replication or DNA transfer, omitting those for integrases and FtsK_SpoIIIE (44). Two heuristics were devised: ICE1 (query has ≥7 ICE HMM matches that account for at least 15% of its proteins), or ICE2 (query has ≥2 ICE HMM matches, accounting for ≥12% of its proteins if <10 kbp or ≥7% of its proteins if ≥10 kbp).…”

Genome sequence ofPseudomonas aeruginosaPAO1161, a PAO1 derivative with the ICEFP2 integrative and conjugative element

“…Remarkably, PAO1161 possesses two large insertions. The 107796 bp insertion in tRNA Lys gene between lepA (PA4541) and clpB (PA4542), flanked by 48 bp repeated sequences, displays a significant similarity to PAPI-1 like integrative conjugative elements (see below) 29,30 . The second 11981 bp insertion between tRNA Met (PA4673.1) and higA (PA4674), flanked by 82 bp repeats, is identical to the prophage-like RGP42 element identified also in MPAO1 and PAO1-DSM 7 .…”

“…Instead, an almost 108 kbp insertion in the chromosome, with a putative mercury resistance operon, was found ( Figure 1B, Figure 3A). The insertion shows similarities (in sequence and organization/composition of operons flanking the putative integration site) to the PAPI-1 family of integrative conjugative elements (ICEs) 29,30,62 abundant in Pseudomonas genomes. ICEs are mobile genetic elements, with a modular structure, encoding complete conjugation machinery (usually a type IV secretion system) allowing transfer of their genome to another host.…”

ThePseudomonas aeruginosaaccessory genome elements influence virulence towardsCaenorhabditis elegans

“…These results show that the presence or absence of the recently identified immune systems bears no apparent 09 relationship with strain virulence. Interestingly, we noted that the gabija system of strain PA14 (genes PA14_60070 and 10 PA14_60080) and strain CF18 (genes #2421 and ID #Q002_01766) are found inside ICEs: PAPI-1 (He et al, 2004) for 11 PA14, and an unnamed ICE (predicted with ICEfinder (Liu et al, 2019)) for CF18. Altogether, these observations 12…”