Genome-wide analyses of the bHLH superfamily in crustaceans: reappraisal of higher-order groupings and evidence for lineage-specific duplications

In silico analysis of crustacean hyperglycemic hormone family G protein-coupled receptor candidates

Ecdysteroid molting hormone synthesis is directed by a pair of molting glands or Y-organs (YOs), and this synthesis is inhibited by molt-inhibiting hormone (MIH). MIH is a member of the crustacean hyperglycemic hormone (CHH) neuropeptide superfamily, which includes CHH and insect ion transport peptide (ITP). It is hypothesized that the MIH receptor is a Class A (Rhodopsin-like) G protein-coupled receptor (GPCR). The YO of the blackback land crab, Gecarcinus lateralis, expresses 49 Class A GPCRs, three of which (Gl-CHHR-A9, -A10, and -A12) were provisionally assigned as CHH-like receptors. CrusTome, a transcriptome database assembled from 189 crustaceans and 12 ecdysozoan outgroups, was used to deorphanize candidate MIH/CHH GPCRs, relying on sequence homology to three functionally characterized ITP receptors (BNGR-A2, BNGR-A24, and BNGR-A34) in the silk moth, Bombyx mori. Phylogenetic analysis and multiple sequence alignments across major taxonomic groups revealed extensive expansion and diversification of crustacean A2, A24, and A34 receptors, designated CHH Family Receptor Candidates (CFRCs). The A2 clade was divided into three subclades; A24 clade was divided into five subclades; and A34 was divided into six subclades. The subclades were distinguished by conserved motifs in extracellular loop (ECL) 2 and ECL3 in the ligand-binding region. Eleven of the 14 subclades occurred in decapod crustaceans. In G. lateralis, seven CFRC sequences, designated Gl-CFRC-A2α1, -A24α, -A24β1, -A24β2, -A34α2, -A34β1, and -A34β2, were identified; the three A34 sequences corresponded to Gl-GPCR-A12, -A9, and A10, respectively. ECL2 in all the CFRC sequences had a two-stranded β-sheet structure similar to human Class A GPCRs, whereas the ECL2 of decapod CFRC-A34β1/β2 had an additional two-stranded β-sheet. We hypothesize that this second β-sheet on ECL2 plays a role in MIH/CHH binding and activation, which will be investigated further with functional assays.

PsPRE1 is a basic helix-loop-helix transcription factor that confers enhanced root growth and tolerance to salt stress in poplar

The basic helix-loop-helix (bHLH) family of transcription factors is one of the largest and oldest transcription factor families in plants. Members of the bHLH family regulate various growth and metabolic processes in plants. We used quantitative trait locus (QTL) mapping and transcriptome sequencing (RNA-seq) to identify PRE1 as a candidate bHLH transcription factor associated with root dry weight (RDW) in poplar. PRE1 was highly expressed in the roots and xylem, and was responsive to gibberellin, salicylic acid, drought, and salt stress. We cloned the PRE1 homolog from Populus simonii 'Tongliao1', referred to as PsPRE1, and transformed it into 84K poplar (Populus alba × Populus glandulosa). The overexpression of PsPRE1 in 84K poplar increased adventitious root development, fresh weight, total root number, and maximum root length. Poplar lines overexpressing PsPRE1 also exhibited enhanced salt tolerance while retaining a normal growth phenotype in the presence of salt stress. Catalase (CAT) activity in the PsPRE1 overexpression lines was higher than that of the wild-type, which may play a role in detoxifying stress-induced hydrogen peroxide production. An RNA-seq analysis of the PsPRE1 overexpression line revealed several differentially expressed genes (DEGs) involved in or related to auxin-, gibberellin-, and salicylic acid pathways, which indicates that the regulation of root development in poplar by PsPRE1 may involve multiple hormones.