Substitution matrix based color schemes for sequence alignment visualization

Kunzmann, Patrick; Mayer, Benjamin E.; Hamacher, Kay

doi:10.1186/s12859-020-3526-6

Cited by 7 publications

(5 citation statements)

References 15 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Conserved amino acids are highlighted and the percentage of identity is shown. The CLUSTAL color scheme was used to color the alignment, reflecting the physicochemical properties of amino acids (Kunzmann et al ., 2020). The asterisk denotes the ARR10 residues that were proposed to directly interact with DNA (Hosoda et al ., 2002) for a comprehensive list of RRB alignments, refer to Supplementary Figure 5.…”

Section: Resultsmentioning

confidence: 99%

Primary multistep phosphorelay activation comprises both cytokinin and abiotic stress responses in Brassicaceae

Mala,

Skalak,

Zemlyanskaya

et al. 2023

Preprint

View full text Add to dashboard Cite

Multistep phosphorelay (MSP) signaling integrates hormonal and environmental signals to control plant development and adaptive responses. The type-ARESPONSE REGULATORs(RRAs), the downstream members of the MSP cascade and cytokinin primary response genes, are supposed to mediate primarily the negative feedback regulation of (cytokinin-induced) MSP signaling. However, the transcriptional data suggest the involvement ofRRAsin stress-related responses as well. By employing evolutionary conservation with the well-characterizedArabidopsis thaliana RRAs, we identified 5 and 38 novel putativeRRAsinBrassica oleraceaandBrassica napus, respectively. Our phylogenetic analysis suggests the existence of gene-specific selective pressure, maintaining the homologs ofARR3, ARR6,andARR16as singletons during the evolution ofBrassica oleraceaandBrassica rapa. We categorizedRRAsbased on the kinetics of their cytokinin-mediated upregulation and observed both similarities and specificities in this type of response across Brassicaceae. Using bioinformatic analysis and experimental data demonstrating the cytokinin responsiveness ofArabidopsis-derivedTCSv2reporter, we unveil the mechanistic conservation of cytokinin-mediated upregulation ofRRAsinBrassica rapaandBrassica napus. Notably, we identify partial cytokinin dependency of cold stress-inducedRRAtranscription, thus corroborating the role of cytokinin signaling in the crop adaptive responses.HighlightsWe identifiedBrassicahomologs ofArabidopsistype-A response regulators (RRAs), demonstrate existence of selective pressure preventing severalRRAsmultiplication during Brassicaceae evolution and describe cytokinin dependency of cold-inducedRRAsupregulation.

show abstract

Section: Resultsmentioning

confidence: 99%

Primary multistep phosphorelay activation comprises both cytokinin and abiotic stress responses in Brassicaceae

Mala,

Skalak,

Zemlyanskaya

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…In addition, the script generates sequence logo plots depicting the proportion of each residue found per site in the alignment. Amino acid residue colors that are proximal in color space, in both the alignments and logo plots, denote similarities in physicochemical characteristics of the corresponding residues ( 61 ). Additionally, a deep-learning algorithm was employed to detect, predict, and annotate the topology of the candidate GPCRs ( 62 ) to delineate intracellular, extracellular, and transmembrane regions.…”

Section: Methodsmentioning

confidence: 99%

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

Kozma,

Pérez-Moreno,

Gandhi

et al. 2024

Front. Endocrinol.

View full text Add to dashboard Cite

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.

show abstract

“…Additionally, the script generated sequence logo plots depicting the proportion of each residue found per alignment site. Amino acid residue colors that are proximal in color space, in both the alignments and logo plots, denote similarities in physicochemical characteristics of the corresponding residues ( 68 ). Additionally, further examination using NCBI’s Conserved Domain Database ( 69 ) assisted with the comparison and identification of sequences.…”

Section: Methodsmentioning

confidence: 99%

Phylogenetic and transcriptomic characterization of insulin and growth factor receptor tyrosine kinases in crustaceans

Flores,

Pérez-Moreno,

Durica

et al. 2024

Front. Endocrinol.

View full text Add to dashboard Cite

Receptor tyrosine kinases (RTKs) mediate the actions of growth factors in metazoans. In decapod crustaceans, RTKs are implicated in various physiological processes, such molting and growth, limb regeneration, reproduction and sexual differentiation, and innate immunity. RTKs are organized into two main types: insulin receptors (InsRs) and growth factor receptors, which include epidermal growth factor receptor (EGFR), fibroblast growth factor receptor (FGFR), vascular endothelial growth factor receptor (VEGFR), and platelet-derived growth factor receptor (PDGFR). The identities of crustacean RTK genes are incomplete. A phylogenetic analysis of the CrusTome transcriptome database, which included all major crustacean taxa, showed that RTK sequences segregated into receptor clades representing InsR (72 sequences), EGFR (228 sequences), FGFR (129 sequences), and PDGFR/VEGFR (PVR; 235 sequences). These four receptor families were distinguished by the domain organization of the extracellular N-terminal region and motif sequences in the protein kinase catalytic domain in the C-terminus or the ligand-binding domain in the N-terminus. EGFR1 formed a single monophyletic group, while the other RTK sequences were divided into subclades, designated InsR1-3, FGFR1-3, and PVR1-2. In decapods, isoforms within the RTK subclades were common. InsRs were characterized by leucine-rich repeat, furin-like cysteine-rich, and fibronectin type 3 domains in the N-terminus. EGFRs had leucine-rich repeat, furin-like cysteine-rich, and growth factor IV domains. N-terminal regions of FGFR1 had one to three immunoglobulin-like domains, whereas FGFR2 had a cadherin tandem repeat domain. PVRs had between two and five immunoglobulin-like domains. A classification nomenclature of the four RTK classes, based on phylogenetic analysis and multiple sequence alignments, is proposed.

show abstract

Substitution matrix based color schemes for sequence alignment visualization

Cited by 7 publications

References 15 publications

Primary multistep phosphorelay activation comprises both cytokinin and abiotic stress responses in Brassicaceae

Primary multistep phosphorelay activation comprises both cytokinin and abiotic stress responses in Brassicaceae

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

Phylogenetic and transcriptomic characterization of insulin and growth factor receptor tyrosine kinases in crustaceans

Contact Info

Product

Resources

About