Elucidating the Function of Novel Components of Extracellular Contractile Injection Systems (eCIS)
Bibliographic record
Abstract
Bacteriophage tails are responsible for delivering viral genomes to bacterial hosts, and they are evolutionary precursors of bacterial extracellular contractile injection systems (eCIS), which are found in diverse bacterial species and some Archaea. In nature, these phage tail-like systems can inject effector proteins into eukaryotic cells, making them promising tools for applications like genome editing and targeted cancer therapies. However, the mechanisms underlying eCIS assembly, effector injection, and cell targeting remain poorly understood. My thesis investigates the assembly pathways of diverse types of eCISs, with an emphasis on understanding the roles of eCIS-specific proteins.The eCIS operons encode proteins homologous to phage proteins but lack tape measure proteins (TMPs), which are a conserved phage feature essential for tail assembly and genome injection. Using heterologous expression, mutagenesis, and transmission electron microscopy (TEM), I analyzed eCIS operons from Yersinia ruckeri and Cellvibrio japonicus. For Y. ruckeri, I demonstrated that Afp6 and Afp14 are critical for tail length determination. This study is the first to report that the deletion of Afp6 or Afp14 results in acorn-like particles, indicating that both proteins are required for tail elongation but not baseplate assembly. My results aligned with a previous study on Serratia entomophila eCIS, which showed that Afp14 is an eCIS-specific TMP. Furthermore, I identified Afp6 as a TMP-assembly factor. C. japonicus carries a distinct type of eCIS that has never been explored. I discovered that the deletion of Afp6 disrupted particle formation completely, suggesting its involvement in baseplate formation. Sequence alignment of related eCIS clusters identified a candidate for a novel TMP-like protein. N-terminal truncations of this protein abolished particle formation, while C-terminal truncations produced defective tails and tube-baseplate assemblies. Additionally, I identified CJ18, a previously uncharacterized eCIS-specific protein essential for assembly, despite lacking homologues in protein databases. These findings demonstrate that C. japonicus and Y. ruckeri eCIS follow distinct assembly pathways. My work provides new insights into the diversity of eCIS types and the roles of eCIS-specific proteins, shedding light on the evolutionary adaptation of eCISs from phages. This study advances our understanding of eCIS assembly mechanisms and establishes a framework for exploring other eCIS components and their biotechnological potential.
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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 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 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".