Data from: Two cGMP-dependent protein kinases have opposing effects on molt-inhibiting hormone regulation of Y-organ ecdysteroidogenesis
Data files
Feb 20, 2025 version files 2.96 MB
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240426_TreeCode.txt
1.42 KB
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240426_V11aligned.fasta
818.16 KB
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240426_V11input.fasta
234.01 KB
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240426_V11KpicSmartGap.fasta
368.46 KB
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240426_V11KpicSmartGapRenamed.treefile
38.15 KB
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240626_PKG1a1groupAligned.fasta
4.84 KB
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240626_PKG1a2groupAligned.fasta
15.66 KB
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240626_PKG1a3groupAligned.fasta
12.49 KB
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240627_PKG1b_Aligned.fasta
9.22 KB
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240628_PKG1a4_Aligned.fasta
10.82 KB
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30-850534263_QSCRL.xls
29.70 KB
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30-850534263.fasta
6.79 KB
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AlignmentScript.txt
577 B
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Cm_PKG_AzentaPrimerSeqs_Aligned.fa
10.91 KB
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Cmaenas_PKG_Nucleotide_Aligned.fasta
36.04 KB
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Glat_PKG_AzentaPrimerSeqs_Aligned.fa
11.65 KB
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Glateralis_PKG_Nucleotide_Aligned.fasta
41.90 KB
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GlCm_Human_Mouse_Nucl_Aligned.fasta
172.27 KB
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GlCm_Human_Mouse_Pep_Aligned.fasta
22.15 KB
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GlCm_PKG1_Peptide_Aligned.fasta
7.08 KB
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GlCm_PKG2_Peptide_Aligned.fa
1.85 KB
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PKG1insertionContigs_Aligned.fasta
27.42 KB
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PKG1insertionContigs.fasta
23.84 KB
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PKGnucleotide.fasta
709.12 KB
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PKGpeptide.fasta
234.90 KB
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PKGSequencesAccessionInfo.xlsx
71.16 KB
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README.md
9.59 KB
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SupplementaryMaterial1_AssayData.xlsx
25.82 KB
Abstract
Decapod crustaceans regulate molting through steroid molting hormones, ecdysteroids, synthesized by the molting gland (Y-organ, YO). Molt-inhibiting hormone (MIH), a neuropeptide synthesized and secreted by the eyestalk ganglia, negatively regulates YO ecdysteroidogenesis. MIH signaling is mediated by cyclic nucleotide second messengers. cGMP-dependent protein kinase (PKG) is the presumed effector of MIH signaling by inhibiting mechanistic Target of Rapamycin Complex 1 (mTORC1)-dependent ecdysteroidogenesis. Phylogenetic analysis of PKG contiguous sequences in CrusTome as well as 35 additional species in NCBI RefSeq, identified 206 PKG1 sequences in 108 species and 59 PKG2 sequences in 53 species. These included four PKG1α splice variants in the N-terminal region that were unique to decapods, as well as PKG1β and PKG2 homologs. In vitro assays using YOs from the blackback land crab (Gecarcinus lateralis) and green shore crab (Carcinus maenas) determined the effects of MIH ± PKG inhibitors on ecdysteroid secretion. A general PKG inhibitor, Rp-8-Br-PET-cGMPS, countered the effects of MIH, as ecdysteroid secretion increased in PKG-inhibited YOs compared to C. maenas YOs incubated with MIH alone. By contrast, a PKG2-specific inhibitor, AP-C5 (4-[4-(1H-Imidazol-1-yl)phenyl]-N-2-propyn-1-yl-2-pyrimidinamine), enhanced the effects of MIH, as ecdysteroid secretion decreased in G. lateralis and C. maenas YOs incubated with AP-C5 and MIH compared to YOs incubated with MIH alone. These data suggest that both PKG1 and PKG2 are activated by MIH, but have opposing effects on mTORC1-dependent ecdysteroidogenesis. A model is proposed in which the dominant role of PKG1 is countered by PKG2, resulting in low ecdysteroid production by the basal YO during intermolt.
https://doi.org/10.5061/dryad.1g1jwsv7b
Description of the data and file structure
This dataset consists of Fasta files of all sequences used for phylogenetic characterization of PKG in crustaceans, and various alignments of isoforms are included; an Excel file with metadata for all sequences used is included and Tree files used to build the PKG phylogenetic tree is included.
Sequencing data for PKG1 isoform validation and PKG2 in G. lateralis and C. maenasAssay data comes from in vitro assays of paired Y-organs from G. lateralis and C. maenas incubated with MIH or MIH ± PKG inhibitors. Hemolymph ecdysteroid (20E) was used to assess the molt stage of the animals, media 20E was measured from the incubation of each YO with the described treatments.
Fasta files include peptide and nucleotide sequences used in this manuscript. Unaligned and aligned files are provided. All alignments were performed using MAFFT-dash.
Sample metadata including the source of each sequence is provided in "PKGSequencesAccessionInfo.xlsx"
Files and variables
File: PKGSequencesAccessionInfo.xlsx
Description: Metadata for all sequences used throughout the manuscript
Variables
- Isoform (Type)
- Contig ID
- Taxon
- Species
- Amino Acid sequence
- Source
- Accession
- Reference
File: GlCm_PKG2_Peptide_Aligned.fa
Description: Alignment of G. lateralis and C. maenas PKG2 protein sequences
File: Glateralis_PKG_Nucleotide_Aligned.fasta
Description: Alignment of G. lateralis PKG1 and PKG2 nucleotide sequences
File: 240426_TreeCode.txt
Description: Code used to align, trim, and build the phylogenetic tree
File: Cmaenas_PKG_Nucleotide_Aligned.fasta
Description: Alignment of C. maenas PKG1 and PKG2 nucleotide sequences
File: GlCm_PKG1_Peptide_Aligned.fasta
Description: Alignment of G. lateralis and C. maenas PKG1 (all isoforms) protein sequences
File: 240426_V11KpicSmartGapRenamed.treefile
Description: Tree file created from "240426_TreeCode.txt"
File: AlignmentScript.txt
Description: Alignment code used to align decapod, human, and mouse sequences
File: GlCm_Human_Mouse_Pep_Aligned.fasta
Description: Alignment of decapod, human, and mouse PKG proteins
File: 240627_PKG1b_Aligned.fasta
Description: Alignment of decapod PKG1β isoforms
File: 240626_PKG1a3groupAligned.fasta
Description: Alignment of decapod PKG1α3 isoforms
File: 240626_PKG1a1groupAligned.fasta
Description: Alignment of decapod PKG1α1 isoforms
File: PKG1insertionContigs_Aligned.fasta
Description: Alignment of PKG1ins isoforms, and their matching sequences that lack the insertion
File: 240626_PKG1a2groupAligned.fasta
Description: Alignment of decapod PKG1α2 isoforms
File: 240628_PKG1a4_Aligned.fasta
Description: Alignment of decapod PKG1α4 isoforms
File: PKG1insertionContigs.fasta
Description: Raw protein sequences used to make the alignment PKG1insertionContigs_Aligned.fasta
File: GlCm_Human_Mouse_Nucl_Aligned.fasta
Description: Alignment of decapod, human, and mouse PKG nucleotide sequences
File: 240426_V11KpicSmartGap.fasta
Description: Trimmed alignment generated by ClipKit using the KpicSmartGap parameter. This file was used in IQ tree to generate the treefile
File: PKGpeptide.fasta
Description: All PKG protein sequences used
File: 240426_V11input.fasta
Description: Input of all PKG protein sequences used to generate the phylogenetic tree
File: PKGnucleotide.fasta
Description: All PKG sequences used, in nucleotide
File: 240426_V11aligned.fasta
Description: Alignment of all PKG protein sequences used before trimming with ClipKit
File: SupplementaryMaterial1_AssayData.xlsx
Description: ELISA data from in vitro Y-organ assays, 20E quantified
Variables
- Exp.
- Experiment
- Hemo 20E (pg/µl)
- Quantity (picograms per microliter) of 20 hydroxyecdysone (20E) in circulating hemolymph for each animal before *in vitro *assays, used to determine molt stage
- Control 20E (pg/µl)
- Quantity (picograms per microliter) of 20E secreted by the control YO into the media over the course of 4.5 hours
- Experimental 20E (pg/µl)
- Quantity (picograms per microliter) of 20E secreted by the experimental YO into the media over the course of 4.5 hours
- %Control_Control
- Percent of the control, for the control samples (Control 20E / Control 20E *100) -> represents the dark gray control bars in Figure 1 in the associated publication
- %Control_Experimental
- Percent of 20E secreted by the experimental YOs relative to the paired control (Experimental 20E / Control 20E *100)
- Mean
- Mean value for each variable for each experiment
- SEM
- Standard error of the mean for each variable for each experiment
Experiments
- Gl_MIH (G. lateralis MIH Assay)
- Control: No treatment
- Experimental: 50 nM MIH
- Gl_Rp8 (G. lateralis MIH ± Rp-8-Br-PET-cGMPs Assay)
- Control: 50 nM MIH
- Experimental: 50 nM MIH + 100 µM Rp-8-Br-PET-cGMP
- Gl_AP-C5 (G. lateralis MIH ± AP-C5 Assay)
- Control: 50 nM MIH
- Experimental: 50 nM MIH + 100 µM AP-C5
- Cm_MIH (C. maenas MIH Assay)
- Control: No treatment
- Experimental: 50 nM MIH
- Cm_Rp8 (C. maenas MIH ± Rp-8-Br-PET-cGMPs Assay)
- Control: 50 nM MIH
- Experimental:
- 50 nM MIH + 1 µM Rp-8-Br-PET-cGMP
- 50 nM MIH + 10 µM Rp-8-Br-PET-cGMP
- 50 nM MIH + 100 µM Rp-8-Br-PET-cGMP
- Cm_AP-C5 (C. maenas MIH ± AP-C5 Assay)
- Control: 50 nM MIH
- Experimental:
- 50 nM MIH + 1 µM AP-C5
- 50 nM MIH + 10 µM AP-C5
- 50 nM MIH + 100 µM AP-C5
File: Glat_PKG_AzentaPrimerSeqs_Aligned.fa
Description: Alignment of G. lateralis PKG sequences identified in transcriptomic data with that sequenced from PCR
File: Cm_PKG_AzentaPrimerSeqs_Aligned.fa
Description: Alignment of C. maenas PKG sequences identified in transcriptomic data with that sequenced from PCR
File: 30-850534263.fasta
Description: Raw sequencing reads
File: 30-850534263_QSCRL.xls
Description: Qscores of raw sequencing reads
Variables
- TrackingNumber
- Tracking number for shipment of PCR products to be sequenced
- DNAType
- Type of DNA sequenced was a purified PCR product
- TubeLabel
- Label of the tube for each sample created by the authors
- DNAName
- Label of the sample, corresponding to sample names in 30-850534263.fasta
- PrimerName
- All primers used were premixed by the authors. Primer sequences are available in the associated publication.
- TemplateName
- Name of the PCR template used for sequencing
- QualitySCore
- "The quality score (QS) is the average QV for all peaks in the trace with an assigned base. It serves as a metric for overall sequence quality. Generally speaking, traces with QS ≥ 40 have good quality; however, it’s advisable to scan the chromatogram to confirm this. Use caution for traces with QS values around 30. Those with QS < 20 are likely to have a weak signal and/or high noise."
- CRL
- Continuous Read Length - "The longest uninterrupted stretch of bases with a running QV average of 20 or higher is known as the continuous read length (CRL)."
- QV20Plus
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"Each assigned base is accompanied by a quality value (QV), which is logarithmically related to the base-calling error:
QV = -10 × log (error probability)
For example, an assigned base with QV = 20 has an error probability of 0.01, or a 1% chance of being incorrectly called. The QV ultimately depends on the shape and signal-to-noise ratio of the peak, and it provides the most objective metric to evaluate the confidence of the base call. Please note these values are closely related to Phred quality scores1,2. By default, Azenta Life Sciences assigns an A, T, G or C when QV ≥ 10 and an N when QV < 10. QVs are embedded in the ab1 file and can be seen in chromatogram viewing software (see example below). High-quality peaks generally have a QV of 20 or higher."
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- SI_A
- Signal Intensity Adenine
- Intensity values are reported in relative fluorescence units.
- SI_C
- Signal Intensity Cytosine
- Intensity values are reported in relative fluorescence units.
- SI_G
- Signal Intensity Guanine
- Intensity values are reported in relative fluorescence units.
- SI_T
- Signal Intensity Thymine
- Intensity values are reported in relative fluorescence units.
- CreatedDate
- Date and time sequencing files were created by Azenta Life Sciences
Code/software
For fasta files and alignments, JalView is recommended for viewing aligned sequences: https://www.jalview.org/
For viewing the tree file, FigTree is recommended http://tree.bio.ed.ac.uk/software/figtree/
To replicate alignments, use MAFFT-dash https://doi.org/10.1093/nar/gkz342
Access information
Other publicly accessible locations of the data:
- N/A
Data was derived from the following sources:
- CrusTome https://doi.org/10.1093/g3journal/jkad098; https://github.com/invertome/crustome
- NCBI
- UniProt
