Prevalence and mobility of integrative and conjugative elements within a Streptomyces natural population

Abstract

Horizontal Gene Transfer (HGT) is a powerful force generating genomic diversity in bacterial populations. HGT in Streptomyces is in large part driven by conjugation thanks to plasmids, Integrative and Conjugative elements (ICEs) and Actinomycete ICEs (AICEs). To investigate the impact of ICE and AICE conjugation on Streptomyces genome evolution, we used in silico and experimental approaches on a set of 11 very closely related strains isolated from a millimeter scale rhizosphere population. Through bioinformatic searches of canonical conjugation proteins, we showed that AICEs are the most frequent integrative conjugative elements, with the central chromosome region being a hotspot for integrative element insertion. Strains exhibited great variation in AICE composition consistent with frequent HGT and/or gene loss. We found that single insertion sites can be home to different elements in different strains (accretion) and conversely, elements belonging to the same family can be found at different insertion sites. A wide variety of cargo genes was present in the AICEs with the potential to mediate strain-specific adaptation (e.g., DNA metabolism and resistance genes to antibiotic and phages). However, a large proportion of AICE cargo genes showed hallmarks of pseudogenization, consistent with deleterious effects of cargo genes on fitness. Pock assays enabled the direct visualization of conjugal AICE transfer and demonstrated the transfer of AICEs between some, but not all, of the isolates. Multiple AICEs were shown to be able to transfer during a single mating event. Although we did not obtain experimental evidence for transfer of the sole chromosomal ICE in this population, genotoxic stress mediated its excision from the chromosome, suggesting its functionality. Our results indicate that AICE-mediated HGT in Streptomyces populations is highly dynamic, with likely impact on strain fitness and the ability to adapt to environmental change.

Correction of non-random mutational biases along a linear bacterial chromosome by the mismatch repair endonuclease NucS

“…RLB1-8 genome was used as reference. The sequence of the five identified integrative and conjugative elements present in RLB1-8 genome ( 56 ) were removed from the transition analysis to avoid bias caused by their possible redundant nucleotide sequences. The 357 kb TIR of RLB1-8 genome was also excluded, as in the MA study.…”

Conjugation mediates large-scale chromosomal transfer inStreptomycesdriving diversification of antibiotic biosynthetic gene clusters

“…Briefly, resistance genes were amplified by PCR from the SuperCos1 (Agilent Technologies) and pIJ6902 44 plasmids respectively (Agilent, USA) (Table S3). Upstream and downstream regions of the targeted chromosomal site were amplified and then assembled by overlap extension-PCR 45 and cloned (site Hin dIII) into the derived pWED2 suicide vector (pWED2* 11 ). The neo or aac(3)IV genes were then inserted and cloned into a Xba I site designed in for that purpose between the cloned upstream and downstream regions.…”

“…These strains that harbored a linear chromosome of ca. 12 Mb were previously shown to contain a great diversity of MGEs, including AICEs capable of effective transfer between strains 11 . Two strain couples (couple A: S1A1-3* x S1D4-23*; couple B: RLB1-9* x SID4-23*; Figure 1 and S1, Table S1) able to reciprocally conjugate were selected for use in this study.…”

“…Pioneering work by Sir David A. Hopwood revealed that recombination in Streptomyces coelicolor A3(2) was stimulated by so-called 'Fertility Factors', a feature which was exploited to produce the first genetic maps in Streptomyces 8 . These fertility factors were further characterized as conjugative plasmids or AICEs (Actinomycete ICEs; the most prevalent MGEs in Streptomyces genomes [9][10][11] ). AICEs and conjugative plasmids in Streptomyces utilize a fundamentally different system for self-transfer compared to canonical conjugative elements.…”

Correction of non-random mutational biases along a linear bacterial chromosome by the mismatch repair endonuclease NucS

“…RLB1-8 genome was used as reference. The sequence of the 5 identified integrative and conjugative elements present in RLB1-8 genome (49) were removed from the transition analysis to avoid bias caused by their possible redundant nucleotide sequences. The 357 kb TIR of RLB1-8 genome was also excluded, as in the MA study.…”