Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection-related chromatin re-organization

Abstract

The unicellular amoeba Acanthamoeba castellanii is ubiquitous in aquatic environments, where it preys on bacteria. The organism also hosts bacterial endosymbionts, some of which are parasitic, including human pathogens such as Chlamydia and Legionella spp. Here we report complete, high quality genome sequences for two extensively studied A. castellanii strains, Neff and C3. Combining long- and short-read data with Hi-C, we generated near chromosome-level assemblies for both strains with 90% of the genome contained in 29 scaffolds for the Neff strain and 31 for the C3 strain. Comparative genomics revealed strain-specific functional enrichment, most notably genes related to signal transduction in the C3 strain, and to viral replication in Neff. Furthermore, we characterized the spatial organization of the A. castellanii genome and showed that it is reorganized during infection by Legionella pneumophila. Infection-dependent chromatin loops were found to be enriched in genes for signal transduction and phosphorylation processes. In genomic regions where chromatin organization changed during Legionella infection, we found functional enrichment for genes associated with metabolism, organelle assembly, and cytoskeleton organization, suggesting that changes in chromosomal folding are associated with host cell biology during infection.

Extreme mitochondrial reduction in a novel group of free-living metamonads

“…For each search, queries included both orthologous sequences from closely related metamonads and, once identified by these methods, the orthologs from other BaSks. The protein sets of the BaSk taxa were also used as queries in BLAST searches against the mitochondrial proteomes from Andalucia godoyi (Genbank accession VRVR00000000; see Gray et al, 2019), Tetrahymena thermophila (predicted protein Genbank accession EAR80512 to EAS07932, see Eisen et al, 2006;Smith et al, 2007), Arabidopsis thaliana (NCBI Bioproject PRJNA10719 and SAMN03081427; see Cheng et al, 2017;The Arabidopsis Genome Iniative, 2000), Homo sapiens (International Human Genome Sequencing Consortium, 2001; mitochondrial proteins from UniProt (GO:0005739)), Acanthamoeba castellanii (NCBI Bioproject PRJNA599339 and PRJNA487265; see Gawryluk et al, 2014;Matthey-Doret et al, 2022), and Saccharomyces cerevisiae (https://www.yeastgenome.org/; see Engel et al, 2014). The top five hits for each query sequence were examined manually.…”

The Status of Molecular Analyses of Isolates of Acanthamoeba Maintained by International Culture Collections

“…How many copies of the 18S rRNA gene are carried within the genome of an amoebae? Recent use of long sequencing technologies on Acanthamoeba indicates that in some isolates the number is exactly two copies, as part of a tandem repeat of the ribosomal RNA gene region [ 45 ]. The sequence of the two copies of the 18S rRNA gene from the Neff isolate differed by a single nucleotide, a difference the result of length in a mononucleotide repeats within the gene [ 45 ].…”

“…Recent use of long sequencing technologies on Acanthamoeba indicates that in some isolates the number is exactly two copies, as part of a tandem repeat of the ribosomal RNA gene region [ 45 ]. The sequence of the two copies of the 18S rRNA gene from the Neff isolate differed by a single nucleotide, a difference the result of length in a mononucleotide repeats within the gene [ 45 ]. In contrast, the two 18S rRNA gene sequences from the C3 isolate (ATCC 50739) differed by 17 nucleotide changes [ 45 ].…”

“…The sequence of the two copies of the 18S rRNA gene from the Neff isolate differed by a single nucleotide, a difference the result of length in a mononucleotide repeats within the gene [ 45 ]. In contrast, the two 18S rRNA gene sequences from the C3 isolate (ATCC 50739) differed by 17 nucleotide changes [ 45 ]. The C3 alleles can be placed into two distinct allele classes.…”

“…Table S8: Inactive cultures lacking any genetic information. Table S9: References for sources of DNA sequence information for cultures of Acanthamoeba from ATCC, CCAP or BEI [ 39 , 45 , 48 , 72 , 73 , 83 , 84 , 85 , 86 , 87 , 88 , 89 , 90 , 91 , 92 , 93 , 94 , 95 , 96 , 97 , 98 , 99 , 100 , 101 , 102 , 103 , 104 , 105 , 106 , 107 , 108 , 109 , 110 , 111 , 112 , 113 , 114 , 115 , 116 , 117 , 118 , 119 , 120 , 121 ].…”