Domain Analysis and Motif Matcher (DAMM): A Program to Predict Selectivity Determinants in <i>Monosiga brevicollis</i> PDZ Domains Using Human PDZ Data
Choanoflagellates are single-celled eukaryotes with complex signaling pathways. They are considered the closest non-metazoan ancestors to mammals and other metazoans and form multicellular-like states called <i>rosettes</i>. The choanoflagellate <i>Monosiga brevicollis</i> co...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2021-10-01
|
| Series: | Molecules |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1420-3049/26/19/6034 |
| _version_ | 1827680626062393344 |
|---|---|
| author | Haley A. Wofford Josh Myers-Dean Brandon A. Vogel Kevin Alexander Estrada Alamo Frederick A. Longshore-Neate Filip Jagodzinski Jeanine F. Amacher |
| author_facet | Haley A. Wofford Josh Myers-Dean Brandon A. Vogel Kevin Alexander Estrada Alamo Frederick A. Longshore-Neate Filip Jagodzinski Jeanine F. Amacher |
| author_sort | Haley A. Wofford |
| collection | DOAJ |
| description | Choanoflagellates are single-celled eukaryotes with complex signaling pathways. They are considered the closest non-metazoan ancestors to mammals and other metazoans and form multicellular-like states called <i>rosettes</i>. The choanoflagellate <i>Monosiga brevicollis</i> contains over 150 PDZ domains, an important peptide-binding domain in all three domains of life (Archaea, Bacteria, and Eukarya). Therefore, an understanding of PDZ domain signaling pathways in choanoflagellates may provide insight into the origins of multicellularity. PDZ domains recognize the C-terminus of target proteins and regulate signaling and trafficking pathways, as well as cellular adhesion. Here, we developed a computational software suite, Domain Analysis and Motif Matcher (DAMM), that analyzes peptide-binding cleft sequence identity as compared with human PDZ domains and that can be used in combination with literature searches of known human PDZ-interacting sequences to predict target specificity in choanoflagellate PDZ domains. We used this program, protein biochemistry, fluorescence polarization, and structural analyses to characterize the specificity of A9UPE9_MONBE, a <i>M. brevicollis</i> PDZ domain-containing protein with no homology to any metazoan protein, finding that its PDZ domain is most similar to those of the DLG family. We then identified two endogenous sequences that bind A9UPE9 PDZ with <100 μM affinity, a value commonly considered the threshold for cellular PDZ–peptide interactions. Taken together, this approach can be used to predict cellular targets of previously uncharacterized PDZ domains in choanoflagellates and other organisms. Our data contribute to investigations into choanoflagellate signaling and how it informs metazoan evolution. |
| first_indexed | 2024-03-10T06:54:17Z |
| format | Article |
| id | doaj.art-aab2a665f1964b859949f5ff798f2e74 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-10T06:54:17Z |
| publishDate | 2021-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-aab2a665f1964b859949f5ff798f2e742023-11-22T16:36:20ZengMDPI AGMolecules1420-30492021-10-012619603410.3390/molecules26196034Domain Analysis and Motif Matcher (DAMM): A Program to Predict Selectivity Determinants in <i>Monosiga brevicollis</i> PDZ Domains Using Human PDZ DataHaley A. Wofford0Josh Myers-Dean1Brandon A. Vogel2Kevin Alexander Estrada Alamo3Frederick A. Longshore-Neate4Filip Jagodzinski5Jeanine F. Amacher6Department of Chemistry, Western Washington University, Bellingham, WA 98225, USADepartment of Computer Science, Western Washington University, Bellingham, WA 98225, USADepartment of Chemistry, Western Washington University, Bellingham, WA 98225, USADepartment of Chemistry, Western Washington University, Bellingham, WA 98225, USADepartment of Chemistry, Western Washington University, Bellingham, WA 98225, USADepartment of Computer Science, Western Washington University, Bellingham, WA 98225, USADepartment of Chemistry, Western Washington University, Bellingham, WA 98225, USAChoanoflagellates are single-celled eukaryotes with complex signaling pathways. They are considered the closest non-metazoan ancestors to mammals and other metazoans and form multicellular-like states called <i>rosettes</i>. The choanoflagellate <i>Monosiga brevicollis</i> contains over 150 PDZ domains, an important peptide-binding domain in all three domains of life (Archaea, Bacteria, and Eukarya). Therefore, an understanding of PDZ domain signaling pathways in choanoflagellates may provide insight into the origins of multicellularity. PDZ domains recognize the C-terminus of target proteins and regulate signaling and trafficking pathways, as well as cellular adhesion. Here, we developed a computational software suite, Domain Analysis and Motif Matcher (DAMM), that analyzes peptide-binding cleft sequence identity as compared with human PDZ domains and that can be used in combination with literature searches of known human PDZ-interacting sequences to predict target specificity in choanoflagellate PDZ domains. We used this program, protein biochemistry, fluorescence polarization, and structural analyses to characterize the specificity of A9UPE9_MONBE, a <i>M. brevicollis</i> PDZ domain-containing protein with no homology to any metazoan protein, finding that its PDZ domain is most similar to those of the DLG family. We then identified two endogenous sequences that bind A9UPE9 PDZ with <100 μM affinity, a value commonly considered the threshold for cellular PDZ–peptide interactions. Taken together, this approach can be used to predict cellular targets of previously uncharacterized PDZ domains in choanoflagellates and other organisms. Our data contribute to investigations into choanoflagellate signaling and how it informs metazoan evolution.https://www.mdpi.com/1420-3049/26/19/6034protein–protein interactionsPDZ domainschoanoflagellatesevolutiontarget selectivityprotein–peptide interactions |
| spellingShingle | Haley A. Wofford Josh Myers-Dean Brandon A. Vogel Kevin Alexander Estrada Alamo Frederick A. Longshore-Neate Filip Jagodzinski Jeanine F. Amacher Domain Analysis and Motif Matcher (DAMM): A Program to Predict Selectivity Determinants in <i>Monosiga brevicollis</i> PDZ Domains Using Human PDZ Data Molecules protein–protein interactions PDZ domains choanoflagellates evolution target selectivity protein–peptide interactions |
| title | Domain Analysis and Motif Matcher (DAMM): A Program to Predict Selectivity Determinants in <i>Monosiga brevicollis</i> PDZ Domains Using Human PDZ Data |
| title_full | Domain Analysis and Motif Matcher (DAMM): A Program to Predict Selectivity Determinants in <i>Monosiga brevicollis</i> PDZ Domains Using Human PDZ Data |
| title_fullStr | Domain Analysis and Motif Matcher (DAMM): A Program to Predict Selectivity Determinants in <i>Monosiga brevicollis</i> PDZ Domains Using Human PDZ Data |
| title_full_unstemmed | Domain Analysis and Motif Matcher (DAMM): A Program to Predict Selectivity Determinants in <i>Monosiga brevicollis</i> PDZ Domains Using Human PDZ Data |
| title_short | Domain Analysis and Motif Matcher (DAMM): A Program to Predict Selectivity Determinants in <i>Monosiga brevicollis</i> PDZ Domains Using Human PDZ Data |
| title_sort | domain analysis and motif matcher damm a program to predict selectivity determinants in i monosiga brevicollis i pdz domains using human pdz data |
| topic | protein–protein interactions PDZ domains choanoflagellates evolution target selectivity protein–peptide interactions |
| url | https://www.mdpi.com/1420-3049/26/19/6034 |
| work_keys_str_mv | AT haleyawofford domainanalysisandmotifmatcherdammaprogramtopredictselectivitydeterminantsinimonosigabrevicollisipdzdomainsusinghumanpdzdata AT joshmyersdean domainanalysisandmotifmatcherdammaprogramtopredictselectivitydeterminantsinimonosigabrevicollisipdzdomainsusinghumanpdzdata AT brandonavogel domainanalysisandmotifmatcherdammaprogramtopredictselectivitydeterminantsinimonosigabrevicollisipdzdomainsusinghumanpdzdata AT kevinalexanderestradaalamo domainanalysisandmotifmatcherdammaprogramtopredictselectivitydeterminantsinimonosigabrevicollisipdzdomainsusinghumanpdzdata AT frederickalongshoreneate domainanalysisandmotifmatcherdammaprogramtopredictselectivitydeterminantsinimonosigabrevicollisipdzdomainsusinghumanpdzdata AT filipjagodzinski domainanalysisandmotifmatcherdammaprogramtopredictselectivitydeterminantsinimonosigabrevicollisipdzdomainsusinghumanpdzdata AT jeaninefamacher domainanalysisandmotifmatcherdammaprogramtopredictselectivitydeterminantsinimonosigabrevicollisipdzdomainsusinghumanpdzdata |