A diversity of uncharacterized reverse transcriptases in bacteria

Genetic variation is critical in microbial immune evasion and drug resistance, but variation has rarely been studied in complex heterogeneous communities such as the human microbiome. To begin to study natural variation, we analyzed DNA viruses present in the lower gastrointestinal tract of 12 human volunteers by determining 48 billion bases of viral DNA sequence. Viral genomes mostly showed low variation, but 51 loci of ∼100 bp showed extremely high variation, so that up to 96% of the viral genomes encoded unique amino acid sequences. Some hotspots of hypervariation were in genes homologous to the bacteriophage BPP-1 viral tail-fiber gene, which is known to be hypermutagenized by a unique reverse-transcriptase (RT)-based mechanism. Unexpectedly, other hypervariable loci in our data were in previously undescribed gene types, including genes encoding predicted Ig-superfamily proteins. Most of the hypervariable loci were linked to genes encoding RTs of a single clade, which we find is the most abundant clade among gut viruses but only a minor component of bacterial RT populations. Hypervariation was targeted to 5′-AAY-3′ asparagine codons, which allows maximal chemical diversification of the encoded amino acids while avoiding formation of stop codons. These findings document widespread targeted hypervariation in the human gut virome, identify previously undescribed types of genes targeted for hypervariation, clarify association with RT gene clades, and motivate studies of hypervariation in the full human microbiome.deep sequencing | diversity-generating retroelement | mutagenesis | major tropism determinant K ey aspects of host-parasite interactions are mediated by targeted changes in DNA. The vertebrate adaptive immune system is based on covalent DNA rearrangements that diversify genes encoding Ig-domain antigen-binding proteins. In response, viral and cellular pathogens encode genetic systems that vary antigens bound by host antigen receptors (1, 2).In this study we begin to characterize patterns of sequence variation in heterogeneous natural communities, using the human microbiome as a model. We chose to study viral samples because they represent a medically important microbiome component, but contain a smaller aggregate genome size than the full microbiome, allowing sequencing to a depth that permits empirical assessment of variation.A newly discovered mechanism of targeted hypermutation, particularly pertinent here, involves the Bordetella bacteriophage BPP-1, which has been shown to vary the sequence of the gene encoding its phage tail fiber to bind divergent cell-surface receptors (3-6). The phage-encoded major tropism determinant (MTD) gene, which encodes the tip of the tail fiber, is subjected to targeted hypermutation by a reverse transcriptase (RT)-dependent mechanism (7,8). The 3′ part of the tail-fiber gene is duplicated in the phage genome, and the duplicated template repeat (TR) is transcribed and reverse-transcribed in an error-prone fashion. The mutated copy is then incorporated into the MTD gene ...

show abstract

“…Five sequences fall into "novel 1" (Fig. 4A), which is most similar to the Unk2 family (19). Seven sequences fall into "novel 2" (Fig.…”

Section: Resultsmentioning

confidence: 98%

“…We next took advantage of the above data to annotate functions of gut virome RT genes. All of the RT sequences previously associated with hypervariable regions (3,6,19) cluster in a monophyletic clade containing the BPP-1 RT (Fig. 4A, cluster marked "DGR" for diversity-generating retroelements).…”

Section: Resultsmentioning

confidence: 99%

Hypervariable loci in the human gut virome

Minot

Grunberg

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

177

184

View full text Add to dashboard Cite

show abstract

“…DB, DNA binding domain; REL, restriction endonuclease-like domain. doi:10.1128/microbiolspec.MDNA3-0050-2014.f6 cellular immunity by synthesizing cDNAs of RNA phages or transcripts of invading DNA elements that are then incorporated into the CRISPR repeats (195,196). Thus, bacterial RTs are engaged in the phage-host arms race, to evade cellular defenses on one hand and to develop immunity to invasive DNA on the other.…”

Section: Figurementioning

confidence: 99%

“…In addition to group II introns, bacteria contain a variety of other retroelements and RTs, which may have evolved from or into group II intron RTs (195,196). These include retrons (197), abortive phage infection (Abi) retroelements (196), diversity generating retroelement RTs (DGRs) (198,199), and RTs associated with some CRISPR-Cas systems (195,196).…”

Section: Group II Intron Evolution Group Ii Intron Origins and Other mentioning

confidence: 99%

“…These include retrons (197), abortive phage infection (Abi) retroelements (196), diversity generating retroelement RTs (DGRs) (198,199), and RTs associated with some CRISPR-Cas systems (195,196). Abi retroelments are host-encoded elements that defend against phage infection (200), while DGRs are bacterial and phage-encoded elements that diversify protein-encoding DNA sequences, such as those involved in cell surface display or phage tropism switching, via an error prone retrohoming mechanism (198,201,202).…”

Section: Group II Intron Evolution Group Ii Intron Origins and Other mentioning

confidence: 99%

See 1 more Smart Citation

Mobile Bacterial Group II Introns at the Crux of Eukaryotic Evolution

2015

View full text Add to dashboard Cite

This review focuses on recent developments in our understanding of group II intron function, the relationships of these introns to retrotransposons and spliceosomes, and how their common features have informed thinking about bacterial group II introns as key elements in eukaryotic evolution. Reverse transcriptase-mediated and host factor-aided intron retrohoming pathways are considered along with retrotransposition mechanisms to novel sites in bacteria, where group II introns are thought to have originated. DNA target recognition and movement by target-primed reverse transcription infer an evolutionary relationship among group II introns, non-LTR retrotransposons, such as LINE elements, and telomerase. Additionally, group II introns are almost certainly the progenitors of spliceosomal introns. Their profound similarities include splicing chemistry extending to RNA catalysis, reaction stereochemistry, and the position of two divalent metals that perform catalysis at the RNA active site. There are also sequence and structural similarities between group II introns and the spliceosome's small nuclear RNAs (snRNAs) and between a highly conserved core spliceosomal protein Prp8 and a group II intron-like reverse transcriptase. It has been proposed that group II introns entered eukaryotes during bacterial endosymbiosis or bacterial-archaeal fusion, proliferated within the nuclear genome, necessitating evolution of the nuclear envelope, and fragmented giving rise to spliceosomal introns. Thus, these bacterial self-splicing mobile elements have fundamentally impacted the composition of extant eukaryotic genomes, including the human genome, most of which is derived from close relatives of mobile group II introns.

show abstract

Telomerase, Retrotransposons, and Evolution

Arkhipova

2012

Telomerases

View full text Add to dashboard Cite

A diversity of uncharacterized reverse transcriptases in bacteria

Cited by 88 publications

References 55 publications

Hypervariable loci in the human gut virome

Hypervariable loci in the human gut virome

Mobile Bacterial Group II Introns at the Crux of Eukaryotic Evolution

Telomerase, Retrotransposons, and Evolution

Contact Info

Product

Resources

About