The antiviral activities of a bacteriophage satellite are mechanistically tied to lateral propagation
Bibliographic record
Abstract
Parasitism is a common evolutionary strategy present in many branches of life, and the study of parasitism has contributed substantially to evolutionary theory. Bacteriophages, viruses that infect bacteria, are one group of parasites that have been particularly valuable models of study. Study of bacteriophages, or phages as they are also known, has vastly improved our understanding of molecular biology. The study of bacterial systems that defend against phages has provided incredibly useful tools for genetic research such as restriction enzymes and CRISPR-Cas. A particularly interesting form of anti-phage defense is hyperparasitism, parasitism of a parasite, by bacteriophage satellites that are endogenous to the bacterial genome. Bacteriophage satellites rely on bacteriophage infection for horizontal mobility while reducing or restricting production of progeny bacteriophage. This allows them to function as immune systems for the cellular populations that encode them. Within this thesis, we identify mechanisms of parasitism and bacteriophage interference by the phage inducible chromosomal island-like element or PLE, a bacteriophage satellite found within some strains of Vibrio cholerae. Using deep sequencing approaches, we have outlined DNA replication and transcriptional programs for both the PLE, and the phage it parasitizes, ICP1. Molecular and phenotypic approaches were also applied to establish how PLE parasitizes ICP1 for its own genome replication and what effect this has on the life cycle of ICP1. We have found that PLE requires ICP1 not just for induction of gene expression, but also for replication of the PLE genome. Consistent with relying on ICP1 machinery for replication and mobilization, PLE does not broadly interfere with ICP1 transcription. The sole exception to this is repression of ICP1 capsid morphogenesis genes, consistent with the PLE remodeling ICP1 virions to fit its smaller genomes. The experiments presented here, along with other recent data, suggest that PLE inhibits ICP1 through multiple mechanisms which have dual functions of also boosting PLE reproduction and mobilization. This thesis provides a foundation for understanding the parasitism strategies of ICP1 and PLE, as well as the mechanisms through which PLE restricts ICP1. Our results suggest that PLE has adapted to interfere with the replication program of ICP1 only to an extent that is beneficial to the PLE, and fit within a context pattern of pathogen and parasite evolutionary patterns.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".