Symposium Presentation Australian Society for Microbiology Annual Scientific Meeting 2024

A distinct quorum-sensing system conserved throughout the genus Mesorhizobium induces transcription of non-coding RNAs targeting 5'-untranslated mRNA regions (104106)

Tahlia R Bastholm 1 , Timothy L Haskett 2 , Daniel G Mediati 3 , Hayley E Knights 4 , Elena Colombi 1 , Robert Trengrove 1 , Yvette Hill 2 , Beatrice AE Panganiban 1 , Louise Thorn 5 , John Sullivan 5 , Clive W Ronson 5 , Jai J Tree 3 , Jason Terpolilli 2 , Philip S Poole 4 , Joshua P Ramsay 1
  1. Curtin University, Perth, WA, Australia
  2. Legume Rhizobium Sciences, Food Futures Institute, Murdoch University, Perth, Western Australia, Australia
  3. School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
  4. Department of Plant Sciences, University of Oxford, Oxford, Oxfordshire, United Kingdom
  5. Microbiology & Immunology, University of Otago, Dunedin, Otago, New Zealand

Mesorhizobium spp. are ubiquitous soil bacteria often capable of forming nitrogen-fixing symbioses with legume plants. Quorum sensing is a form of chemical cell-cell communication bacteria use to coordinate a variety of activities, often those which serve a public good in clonal populations or benefit from coordinated population-level expression. We bioinformatically identified a LuxR/LuxI-family N-acyl-homoserine lactone (AHL) quorum sensing system conserved in 206/214 unique sequenced Mesorhizobium spp., named here MQS. In addition to the regulator gene mqsR and AHL-synthase gene mqsI, the MQS locus includes a conserved mqsC gene encoding a putative crotonase-family protein. Mutational analysis and mass spectrometry revealed both MqsI and MqsC together synthesise the diunstaturated N-((2E,4E)-2,4-dodecadienoyl) homoserine lactone (abbreviated 2,4-trans-C12-HSL), making MQS the only known LuxRI-family quorum sensing system to encode two proteins for AHL-synthesis. MqsR-dependent promoters responded most highly to synthesised 2,4-trans-C12-HSL compared to other C12-HSL derivatives or short-chain AHLs, suggesting Mesorhizobium spp. utilise 2,4-trans-C12-HSL to communicate specifically with each other. RNA transcriptome sequencing of mqsRIC-mutants revealed very few changes in the abundance of protein-coding mRNAs but inspection of mapped RNA reads led to the identification of seven novel non-coding RNA genes scattered throughout the chromosome, mqsRNA1-mqsRNA7. Transcription of mqsRNA1-mqsRNA7 required mqsR and 2,4-trans-C12-HSL. Interestingly, the eight (of 214) Mesorhizobium spp. lacking the mqsRIC locus also lacked mqsRNA1-mqsRNA7. Promoter truncations and transcriptional fusions revealed MqsR directly activates transcription downstream of a “GYGATCRC” motif, likely representing the MqsR binding site. The small RNA chaperone Hfq was used to capture and sequence small RNA interactions with target mRNAs (termed Hfq-CLASH). These analyses reveal that the most abundant MqsR-activated non-coding RNA, mqsRNA7, tentatively binds the 5-untranslated regions of numerous mRNA transcripts coding for proteins involved in nutrient uptake and membrane transport.