Thermodynamic matchers for the construction of the cuckoo RNA family

Abstract

RNA family models describe classes of functionally related, non-coding RNAs based on sequence and structure conservation. The most important method for modeling RNA families is the use of covariance models, which are stochastic models that serve in the discovery of yet unknown, homologous RNAs. However, the performance of covariance models in finding remote homologs is poor for RNA families with high sequence conservation, while for families with high structure but low sequence conservation, these models are difficult to built in the first place. A complementary approach to RNA family modeling involves the use of thermodynamic matchers. Thermodynamic matchers are RNA folding programs, based on the established thermodynamic model, but tailored to a specific structural motif. As thermodynamic matchers focus on structure and folding energy, they unfold their potential in discovering homologs, when high structure conservation is paired with low sequence conservation. In contrast to covariance models, construction of thermodynamic matchers does not require an input alignment, but requires human design decisions and experimentation, and hence, model construction is more laborious. Here we report a case study on an RNA family that was constructed by means of thermodynamic matchers. It starts from a set of known but structurally different members of the same RNA family. The consensus secondary structure of this family consists of 2 to 4 adjacent hairpins. Each hairpin loop carries the same motif, CCUCCUCCC, while the stems show high variability in their nucleotide content. The present study describes (1) a novel approach for the integration of the structurally varying family into a single RNA family model by means of the thermodynamic matcher methodology, and (2) provides the results of homology searches that were conducted with this model in a wide spectrum of bacterial species.

A conserved α‐proteobacterial small RNA contributes to osmoadaptation and symbiotic efficiency of rhizobia on legume roots

“…The non-coding transcriptome of the a-rhizobia S. meliloti has been extensively characterized in recent years, but the regulatory role of the vast majority of the newly identified sRNAs remains to be elucidated (Jim enez-Zurdo and . In this work, we have genetically approached the function of a yet uncharacterized S. meliloti trans-sRNA, NfeR1, which is widespread in phylogenetically related a-proteobacteria interacting with eukaryotic hosts (del Val et al, 2012;Reinkensmeier and Giegerich, 2015). Its expression profile and associated phenotypes placed NfeR1 as a novel regulator of a salt stress response influencing both osmoadaptation and the overall symbiotic performance of S. meliloti on alfalfa roots.…”

“…In this work, we have approached the function of a new S. meliloti trans-sRNA, referred to as SmrC14, Smr14C2 or SmelC397 in previous independent genome-wide screens (del Val et al, 2007;Schl€ uter et al, 2010;del Val et al, 2012). Homologues of this sRNA are commonly encoded in multiple copies in the genomes of bacteria belonging to the Rhizobiaceae, Brucellaceae and Phyllobacteriaceae families, integrating the so-called ar14 family of a-proteobacterial sRNAs (del Val et al, 2012;Reinkensmeier and Giegerich, 2015). Members of this family share a predicted secondary structure consisting of three adjacent hairpins, each carrying the unpaired anti Shine-Dalgarno (aSD) motif 'CCUCCUCCC' but differing highly in the primary nucleotide sequence of the respective stems (del Val et al, 2012;Reinkensmeier and Giegerich, 2015;Rivas et al, 2017).…”

“…Homologues of this sRNA are commonly encoded in multiple copies in the genomes of bacteria belonging to the Rhizobiaceae, Brucellaceae and Phyllobacteriaceae families, integrating the so-called ar14 family of a-proteobacterial sRNAs (del Val et al, 2012;Reinkensmeier and Giegerich, 2015). Members of this family share a predicted secondary structure consisting of three adjacent hairpins, each carrying the unpaired anti Shine-Dalgarno (aSD) motif 'CCUCCUCCC' but differing highly in the primary nucleotide sequence of the respective stems (del Val et al, 2012;Reinkensmeier and Giegerich, 2015;Rivas et al, 2017). Six putative ar14 loci were identified in the S. meliloti reference genome but only the 123-nt long Smr14C2 transcript (coordinates 1 667 613 to 1 667 491 in the Rm1021 chromosome) has been reliable detected by Northern hybridization, being particularly abundant in nodules (del Val et al, 2007;Roux et al, 2014).…”

Riboregulation in Nitrogen-Fixing Endosymbiotic Bacteria

“…CM-based phylogenetic distribution of other 57 S. meliloti trans-sRNAs without associated functional evidence has been also addressed by several independent studies [43][44][45][46]. In two particular cases where high secondary structure but low sequence conservation hindered construction of the CMs, RNA families were modeled using a complementary thermodynamic matchers (TDMs) based approach [43,44]. TDMs are RNA predictors that ignore sequence conservation in some parts, rather scoring the folding energy of conserved motifs elsewhere in the structure.…”

“…To date, phenotyping of knock-out mutants has revealed putative symbiotic functions for only one chromosomally encoded S. meliloti regulatory trans-sRNA, identified in early genome-wide screens as Smr14C2 or SmelC397, and later renamed NfeR1 (nodule formation efficiency RNA) to reflect this fact [20,26,92]. NfeR1 belongs to the so-called αr14 family of α-proteobacterial sRNAs (Table 1), which is represented in most plant symbionts, phytopathogens and mammal pathogens within Rhizobiaceae, Brucellaceae and Phyllobacteriaceae bacterial families [44,46]. αr14 sRNAs share a predicted secondary structure consisting of three hairpins with hypervariable nucleotide content in the stems and the aSD motif unpaired in all the loops [44,46].…”