Project 3
Small RNA landscape of insect symbioses: Convergence and divergence across hosts and symbionts
Supervisors:
Mariana Galvão Ferrarini (main supervisor)
Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena
Martin Kaltenpoth (co-supervisor)
Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena
Background:
Many insects rely on bacterial symbionts housed within specialized host cells or organs called bacteriomes. Maintaining these intimate partnerships requires coordinated control of gene expression: the host must regulate symbiont abundance and activity, while the symbiont must adapt to life inside host cells. Yet the regulators that achieve this fine-tuned control remain poorly understood. Small regulatory RNAs (sRNAs) are strong candidates on both sides of this interface. In insects, microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs) and small interfering RNAs (siRNAs) contribute to gene regulation, defense and responses to foreign genetic material. In bacteria, sRNAs regulate stress responses and metabolism, and some are retained even in the highly reduced genomes of obligate symbionts. Small RNAs can also regulate genes across kingdoms, suggesting that they may enable communication between insect hosts and their bacterial partners. Although previous studies have identified host miRNAs in symbiotic organs and catalogued bacterial sRNAs in a few reduced-genome symbionts, these findings remain restricted to individual systems. It therefore remains unclear whether sRNA-based control is a general feature of insect symbioses or a lineage-specific solution.
Project description:
This project addresses this open question by comparing small RNAs across several independent insect symbioses. To do so, the PhD student will profile host and symbiont-derived sRNAs, together with mRNAs, in symbiotic organs and control tissues of different insect species, including symbiont-free relatives or aposymbiotic lines where available. The objectives will be (1) annotation of host miRNA, piRNA and siRNA repertoires and of symbiont-derived sRNAs, (2) host and cross-kingdom target prediction integrated with expression data, (3) analysis of the evolutionary conservation of sRNA families and their targets across lineages, and (4) functional validation of selected candidates.
The project will be integrated in the larger group of scientists working on the molecular control and evolution of insect-bacteria symbioses in the department. The focus of the project, including the choice of insect systems, will be co-developed with the successful applicant. The range of methods will include bioinformatics workflows including bioinformatic annotation, comparative analysis of sRNAs, target prediction, and phylogenetic analyses, as well as wet lab experiments such as dissection of symbiotic organs, small RNA and mRNA sequencing, validation of sRNA expression and localization, and monitoring of symbiont titer and symbiosis-related host traits.
Candidate profile:
• a deep interest in the molecular and evolutionary biology of insect-microbe interactions
• a background in bioinformatics, molecular biology, or both, and the willingness to learn the other side
• experience with RNA work or analysis of sequencing data is an advantage
• attention to detail and patience for handling small insect tissues and large datasets
• critical scientific thinking skills
• curiosity, creativity, and ambition
• excellent time management and organizational skills
• the ability and willingness to interact with other scientists in the group
• proficiency in written and spoken English and good communication skills
Reading:
Bartel, D. P. Metazoan microRNAs. Cell 173, 20-51 (2018).
Bhattacharyya, S. et al. Regulation of beneficial intracellular symbionts in insects. Curr. Opin. Insect Sci. 77, 101566 (2026).
Dell'Aglio, E., Ferrarini, M. G. & Rebollo, R. Epigenetics and non-coding RNAs in host-endosymbiont interactions: insights from Wolbachia and beyond. Curr. Opin. Insect Sci. 74, 101464 (2026).
Feng, H. et al. microRNA regulation in an ancient obligate endosymbiosis. Mol. Ecol. 27, 1777-1793 (2018).
Hansen, A. K. & Degnan, P. H. Widespread expression of conserved small RNAs in small symbiont genomes. ISME J. 8, 2490-2501 (2014).
Mayoral, J. G. et al. Wolbachia small noncoding RNAs and their role in cross-kingdom communications. Proc. Natl. Acad. Sci. 111, 18721-18726 (2014).
Wagner, E. G. H. & Romby, P. Small RNAs in bacteria and archaea: who they are, what they do, and how they do it. Adv. Genet. 90, 133-208 (2015).