Rapid de novo evolution of lysis genes in single-stranded RNA phages

Chamakura, Karthik R.; Tran, Jennifer S.; O’Leary, Chandler; Lisciandro, Hannah G.; Antillon, Sophia F.; Garza, Kameron D.; Tran, Elizabeth; Min, Lorna; Young, Ralph H.

doi:10.1038/s41467-020-19860-0

Cited by 20 publications

(21 citation statements)

References 36 publications

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“…One such mechanism is de novo evolution, the birth of new genes from previously non-genic or intronic regions, which is now a widely acknowledged source of protein-coding and RNA genes [3][4][5]. Although de novo origination was once considered an unlikely event, catalogs of de novo genes have now been published for an expansive range of species [6][7][8][9][10][11][12][13]. Multiple models explain how protein-coding de novo genes may acquire both an open reading frame (ORF) and regulatory sequences permitting transcription [14][15][16][17].…”

Section: Introductionmentioning

confidence: 99%

A putative de novo evolved gene required for spermatid chromatin condensation in Drosophila melanogaster

et al. 2021

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Comparative genomics has enabled the identification of genes that potentially evolved de novo from non-coding sequences. Many such genes are expressed in male reproductive tissues, but their functions remain poorly understood. To address this, we conducted a functional genetic screen of over 40 putative de novo genes with testis-enriched expression in Drosophila melanogaster and identified one gene, atlas, required for male fertility. Detailed genetic and cytological analyses showed that atlas is required for proper chromatin condensation during the final stages of spermatogenesis. Atlas protein is expressed in spermatid nuclei and facilitates the transition from histone- to protamine-based chromatin packaging. Complementary evolutionary analyses revealed the complex evolutionary history of atlas. The protein-coding portion of the gene likely arose at the base of the Drosophila genus on the X chromosome but was unlikely to be essential, as it was then lost in several independent lineages. Within the last ~15 million years, however, the gene moved to an autosome, where it fused with a conserved non-coding RNA and evolved a non-redundant role in male fertility. Altogether, this study provides insight into the integration of novel genes into biological processes, the links between genomic innovation and functional evolution, and the genetic control of a fundamental developmental process, gametogenesis.

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Section: Introductionmentioning

confidence: 99%

A putative de novo evolved gene required for spermatid chromatin condensation in Drosophila melanogaster

et al. 2021

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“…A 2 is highly asymmetric in shape and spans 110 Å in length while bound to the phage genome. The A 2 takes the position of a Cp-dimer and disrupts the perfect icosahedral symmetric shape of the capsid with the triangulation number of T = 3 [71][72][73]. The structural organization of the A 2 has two distinct regions, namely an α-helical part (with four-helix core) and a β stranded part (with seven-stranded sheet).…”

Section: Structure and Domainmentioning

confidence: 99%

Uniqueness of RNA Coliphage Qβ Display System in Directed Evolutionary Biotechnology

Nchinda

Al-Atoom

Coats

et al. 2021

Viruses

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Phage display technology involves the surface genetic engineering of phages to expose desirable proteins or peptides whose gene sequences are packaged within phage genomes, thereby rendering direct linkage between genotype with phenotype feasible. This has resulted in phage display systems becoming invaluable components of directed evolutionary biotechnology. The M13 is a DNA phage display system which dominates this technology and usually involves selected proteins or peptides being displayed through surface engineering of its minor coat proteins. The displayed protein or peptide’s functionality is often highly reduced due to harsh treatment of M13 variants. Recently, we developed a novel phage display system using the coliphage Qβ as a nano-biotechnology platform. The coliphage Qβ is an RNA phage belonging to the family of Leviviridae, a long investigated virus. Qβ phages exist as a quasispecies and possess features making them comparatively more suitable and unique for directed evolutionary biotechnology. As a quasispecies, Qβ benefits from the promiscuity of its RNA dependent RNA polymerase replicase, which lacks proofreading activity, and thereby permits rapid variant generation, mutation, and adaptation. The minor coat protein of Qβ is the readthrough protein, A1. It shares the same initiation codon with the major coat protein and is produced each time the ribosome translates the UGA stop codon of the major coat protein with the of misincorporation of tryptophan. This misincorporation occurs at a low level (1/15). Per convention and definition, A1 is the target for display technology, as this minor coat protein does not play a role in initiating the life cycle of Qβ phage like the pIII of M13. The maturation protein A2 of Qβ initiates the life cycle by binding to the pilus of the F+ host bacteria. The extension of the A1 protein with a foreign peptide probe recognizes and binds to the target freely, while the A2 initiates the infection. This avoids any disturbance of the complex and the necessity for acidic elution and neutralization prior to infection. The combined use of both the A1 and A2 proteins of Qβ in this display system allows for novel bio-panning, in vitro maturation, and evolution. Additionally, methods for large library size construction have been improved with our directed evolutionary phage display system. This novel phage display technology allows 12 copies of a specific desired peptide to be displayed on the exterior surface of Qβ in uniform distribution at the corners of the phage icosahedron. Through the recently optimized subtractive bio-panning strategy, fusion probes containing up to 80 amino acids altogether with linkers, can be displayed for target selection. Thus, combined uniqueness of its genome, structure, and proteins make the Qβ phage a desirable suitable innovation applicable in affinity maturation and directed evolutionary biotechnology. The evolutionary adaptability of the Qβ phage display strategy is still in its infancy. However, it has the potential to evolve functional domains of the desirable proteins, glycoproteins, and lipoproteins, rendering them superior to their natural counterparts.

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“…Early studies on model ssDNA and ssRNA phages showed that native sgl genes are hard to identify through genomic approaches 12,15 . Sgls are typically small, embedded within other coding regions, and bear little sequence similarity to each other 3,[16][17][18] . Linking a gene to its mechanism of action has most often been accomplished using classical genetic selections 7,9 .…”

Section: Introductionmentioning

confidence: 99%

Parallel multicopy-suppressor screens reveal convergent evolution of phage-encoded single gene lysis proteins

Adler

Chamakura

Carion

et al. 2022

Preprint

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In contrast to canonical dsDNA phages, lysis in ssRNA Fiersviridae and ssDNA Microviridae phages is encoded by a minimal single gene (sgl), to meet the size constraints of some of the smallest genomes on earth. To achieve lysis, Sgl proteins exploit evolutionary "weak spots" in the bacterial cell wall by inhibiting specific steps in cell wall synthesis. Although a handful of these proteins have been characterized, the potentially diverse "weak spots" targeted by most Sgls remains enigmatic. Here, we repurpose Dub-seq for genome-wide assessment of host suppressors of Sgl activity and apply to eight diverse Sgls awaiting molecular target characterization. In addition to known molecular mechanisms, we discover a complex network of suppressors across the spectrum of genes involved in cell wall biogenesis. We highlight the first case of Sgl convergent evolution between unrelated proteins by determining the molecular target of SglPP7 as MurJ, suggesting the existence of universal "weak spots" in the bacterial cell wall.

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Rapid de novo evolution of lysis genes in single-stranded RNA phages

Cited by 20 publications

References 36 publications

A putative de novo evolved gene required for spermatid chromatin condensation in Drosophila melanogaster

A putative de novo evolved gene required for spermatid chromatin condensation in Drosophila melanogaster

Uniqueness of RNA Coliphage Qβ Display System in Directed Evolutionary Biotechnology

Parallel multicopy-suppressor screens reveal convergent evolution of phage-encoded single gene lysis proteins

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