scholarly journals Origin and Isoform Specific Functions of Exchange Proteins Directly Activated by cAMP: A Phylogenetic Analysis

Cells ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2750
Author(s):  
Zhuofu Ni ◽  
Xiaodong Cheng
Keyword(s):  
Phylogenetic Analysis ◽  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Sequence Diversity ◽  
Sequence Motifs ◽  
Nucleotide Exchange ◽  
Animal Kingdom ◽  
Specific Sequence ◽  
Guanine Nucleotide Exchange ◽  
The Individual

Exchange proteins directly activated by cAMP (EPAC1 and EPAC2) are one of the several families of cellular effectors of the prototypical second messenger cAMP. To understand the origin and molecular evolution of EPAC proteins, we performed a comprehensive phylogenetic analysis of EPAC1 and EPAC2. Our study demonstrates that unlike its cousin PKA, EPAC proteins are only present in multicellular Metazoa. Within the EPAC family, EPAC1 is only associated with chordates, while EPAC2 spans the entire animal kingdom. Despite a much more contemporary origin, EPAC1 proteins show much more sequence diversity among species, suggesting that EPAC1 has undergone more selection and evolved faster than EPAC2. Phylogenetic analyses of the individual cAMP binding domain (CBD) and guanine nucleotide exchange (GEF) domain of EPACs, two most conserved regions between the two isoforms, further reveal that EPAC1 and EPAC2 are closely clustered together within both the larger cyclic nucleotide receptor and RAPGEF families. These results support the notion that EPAC1 and EPAC2 share a common ancestor resulting from a fusion between the CBD of PKA and the GEF from RAPGEF1. On the other hand, the two terminal extremities and the RAS-association (RA) domains show the most sequence diversity between the two isoforms. Sequence diversities within these regions contribute significantly to the isoform-specific functions of EPACs. Importantly, unique isoform-specific sequence motifs within the RA domain have been identified.

scholarly journals Placenta-Specific Protein 1 Is Conserved throughout the Placentalia under Purifying Selection

2014 ◽  
Vol 2014 ◽  
pp. 1-5 ◽  
Author(s):  
Eric J. Devor
Keyword(s):  
Phylogenetic Analysis ◽  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Mammalian Species ◽  
Purifying Selection ◽  
Specific Protein ◽  
Mammal Species ◽  
Crucial Component ◽  
Successful Group ◽  
The Common

Placental mammals (Placentalia) are a very successful group that, today, comprise 94% of all mammalian species. Recent phylogenetic analyses, coupled with new, quite complete fossils, suggest that the crown orders were all established rapidly from a common ancestor just after the Cretaceous/Tertiary (K/T) boundary 65 million years ago. Extensive molecular and morphologic evidence has led to a description of the common ancestor of all Placentalia in which a two-horned uterus and a hemochorial placenta are present. Thus, the process of placentation in which the placenta invades and anchors to the uterine epithelium was already established. One factor that has been suggested as a crucial component of this process is placenta-specific protein 1 (PLAC1). A phylogenetic analysis of the PLAC1 protein in 25 placental mammal species, representing nine of the sixteen crown orders of the Placentalia, suggests that this protein was present in the placental common ancestor in the form we see it today, that it evolved in the Placentalia and has been subject to the effects of purifying selection since its appearance.

scholarly journals Phylogenetic analysis of Andinia (Pleurothallidinae; Orchidaceae) and a systematic re-circumscription of the genus

Phytotaxa ◽  
2017 ◽  
Vol 295 (2) ◽  
pp. 101 ◽  
Author(s):  
MARK WILSON ◽  
GRAHAM S. FRANK ◽  
LOU JOST ◽  
ALEC M. PRIDGEON ◽  
SEBASTIAN VIEIRA-URIBE ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Convergent Evolution ◽  
Type Species ◽  
Floral Morphology ◽  
Phylogenetic Analyses ◽  
Evolutionary Diversification ◽  
The Andes ◽  
Deceit Pollination ◽  
Nuclear Its ◽  
The Individual

Most of the species studied in this paper have previously been placed in either Pleurothallis or Lepanthes. However, at one time or another, members of the group have also been placed in the genera Andinia, Brachycladium, Lueranthos, Masdevalliantha, Neooreophilus, Oreophilus, Penducella, Salpistele and Xenosia. Phylogenetic analyses of nuclear ITS and plastid matK sequences indicate that these species form a strongly supported clade that is only distantly related to Lepanthes and is distinct from Pleurothallis and Salpistele. Since this clade includes the type species of Andinia, A. dielsii, and it has taxonomic precedence over all other generic names belonging to this group, Andinia is re-circumscribed and expanded to include 72 species segregated into five subgenera: Aenigma, Andinia, Brachycladium, Masdevalliantha and Minuscula. The required taxonomic transfers are made herein. We hypothesize that convergent evolution towards a similar pollinator syndrome involving deceit pollination via pseudocopulation by Diptera resulted in a similar floral morphology between species of subgenus Brachycladium and species of Lepanthes; hence the prior placement of the species of subgenus Brachycladium in Lepanthes. Species of the re-circumscribed Andinia are confined exclusively to the Andes, ranging from about 1,200 to 3,800 m, from Colombia south to Bolivia, making the generic name very apt. Elevational distributions of the individual clades are discussed in relation to the possible evolutionary diversification of the most species-rich clade, subgenus Brachycladium.

scholarly journals Ancient complement and lineage-specific evolution of the Sec7 ARF GEF proteins in eukaryotes

2019 ◽  
Vol 30 (15) ◽  
pp. 1846-1863 ◽  
Author(s):  
Shweta V. Pipaliya ◽  
Alexander Schlacht ◽  
Christen M. Klinger ◽  
Richard A. Kahn ◽  
Joel Dacks
Keyword(s):  
Membrane Trafficking ◽  
Protein Function ◽  
Phylogenetic Analyses ◽  
Guanine Nucleotide Exchange Factors ◽  
Nucleotide Exchange ◽  
Cellular Processes ◽  
Guanine Nucleotide Exchange ◽  
Nucleotide Exchange Factors ◽  
Gtpase Activating Proteins ◽  
Functionally Diverse

Guanine nucleotide exchange factors (GEFs) are the initiators of signaling by every regulatory GTPase, which in turn act to regulate a wide array of essential cellular processes. To date, each family of GTPases is activated by distinct families of GEFs. Bidirectional membrane trafficking is regulated by ADP-ribosylation factor (ARF) GTPases and the development throughout eukaryotic evolution of increasingly complex systems of such traffic required the acquisition of a functionally diverse cohort of ARF GEFs to control it. We performed phylogenetic analyses of ARF GEFs in eukaryotes, defined by the presence of the Sec7 domain, and found three subfamilies (BIG, GBF1, and cytohesins) to have been present in the ancestor of all eukaryotes. The four other subfamilies (EFA6/PSD, IQSEC7/BRAG, FBX8, and TBS) are opisthokont, holozoan, metazoan, and alveolate/haptophyte specific, respectively, and each is derived from cytohesins. We also identified a cytohesin-derived subfamily, termed ankyrin repeat-containing cytohesin, that independently evolved in amoebozoans and members of the SAR and haptophyte clades. Building on evolutionary data for the ARF family GTPases and their GTPase-­activating proteins allowed the generation of hypotheses about ARF GEF protein function(s) as well as a better understanding of the origins and evolution of cellular complexity in eukaryotes.

Morphological reassessment and molecular assessment of Sargassum (Fucales: Phaeophyceae) species from the Gulf of California, Mexico

Phytotaxa ◽  
2014 ◽  
Vol 183 (4) ◽  
pp. 201 ◽  
Author(s):  
GABRIELA ANDRADE-SORCIA ◽  
RAFAEL RIOSMENA-RODRIGUEZ ◽  
RAQUEL MUÑIZ-SALAZAR ◽  
JUAN MANUEL LÓPEZ-VIVAS ◽  
GA HUN BOO ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Brown Algae ◽  
Gulf Of California ◽  
Phylogenetic Analyses ◽  
The Pacific ◽  
Pacific Side ◽  
Molecular Studies ◽  
Molecular Assessment ◽  
The Individual

Systematic molecular studies have not been performed on ecologically important brown algae (Sargassum) in the Gulf of California, Mexico, where 42 specific and infraspecific names have been recorded within this genus. We conducted phylogenetic analyses of nuclear ribosomal ITS and mitochondrial cox1 and cox3 sequences, along with detailed morphological observations of Sargassum collected in the Gulf of California. We confirmed the presence of six species, five previously described—S. herporhizum, S. horridum, S. johnstonii, S. lapazeanum, and S. sinicola, as well as the newly described Sargassum ulixei sp. nov. which is characterized by terete primary axes arising from the stipe, lanceolate to elliptical sessile ecostate blades with smooth margins, cryptostomata, ellipsoidal vesicles with a short mucron, and cylindrical to ellipsoidal receptacles. The individual analyses and subsequent phylogenetic analysis recognized two groups previously described by Dawson, one as Sargassum and other as Horridum. Our studies suggest that the Gulf of California is a region with endemic Sargassum species, and is clearly distinguished from the Pacific side of Baja California, where recently introduced species are common. Based on phylogenetic relationships, we propose two geographical origins for the Sargassum from the Gulf of California: a first group originating from the proto-Gulf, related to species from the northern hemisphere (including five species); and a second group, containing S. sinicola, introduced when the southern end opened at a later stage. 

scholarly journals Ras Binding Triggers Ubiquitination of the Ras Exchange Factor Ras-GRF2

2001 ◽  
Vol 21 (6) ◽  
pp. 2107-2117 ◽  
Author(s):  
Carmen L. de Hoog ◽  
Jackie A. Koehler ◽  
Marni D. Goldstein ◽  
Paul Taylor ◽  
Daniel Figeys ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Small Gtpase ◽  
Dominant Negative ◽  
26S Proteasome ◽  
Guanine Nucleotide ◽  
Sequence Motifs ◽  
Nucleotide Exchange ◽  
Exchange Factor ◽  
Guanine Nucleotide Exchange

ABSTRACT Ras is a small GTPase that is activated by upstream guanine nucleotide exchange factors, one of which is Ras-GRF2. GRF2 is a widely expressed protein with several recognizable sequence motifs, including a Ras exchanger motif (REM), a PEST region containing a destruction box (DB), and a Cdc25 domain. The Cdc25 domain possesses guanine nucleotide exchange factor activity and interacts with Ras. Herein we examine if the DB motif in GRF2 results in proteolysis via the ubiquitin pathway. Based on the solved structure of the REM and Cdc25 regions of the Son-of-sevenless (Sos) protein, the REM may stabilize the Cdc25 domain during Ras binding. The DB motif of GRF2 is situated between the REM and the Cdc25 domains, tempting speculation that it may be exposed to ubiquitination machinery upon Ras binding. GRF2 protein levels decrease dramatically upon activation of GRF2, and dominant-negative Ras induces degradation of GRF2, demonstrating that signaling downstream of Ras is not required for the destruction of GRF2 and that binding to Ras is important for degradation. GRF2 is ubiquitinated in vivo, and this can be detected using mass spectrometry. In the presence of proteasome inhibitors, Ras-GRF2 accumulates as a high-molecular-weight conjugate, suggesting that GRF2 is destroyed by the 26S proteasome. Deleting the DB reduces the ubiquitination of GRF2. GRF2 lacking the Cdc25 domain is not ubiquitinated, suggesting that a protein that cannot bind Ras cannot be properly targeted for destruction. Point mutations within the Cdc25 domain that eliminate Ras binding also eliminate ubiquitination, demonstrating that binding to Ras is necessary for ubiquitination of GRF2. We conclude that conformational changes induced by GTPase binding expose the DB and thereby target GRF2 for destruction.

scholarly journals Barley guanine nucleotide exchange factor HvGEF14 is an activator of the susceptibility factor HvRACB and supports host cell entry by Blumeria graminis f.sp. hordei

2021 ◽  
Author(s):  
Adriana Trutzenberg ◽  
Stefan Engelhardt ◽  
Ralph Hueckelhoven
Keyword(s):  
Phylogenetic Analyses ◽  
Blumeria Graminis ◽  
Binding Motif ◽  
Cell Periphery ◽  
Type I ◽  
Guanine Nucleotide ◽  
Nucleotide Exchange ◽  
In Planta ◽  
Parasitic Fungi ◽  
Guanine Nucleotide Exchange

In barley (Hordeum vulgare), the function of ROPs appears central to polar cell development and the interaction outcome with parasitic fungi but little is known about ROP activation. Guanine nucleotide exchange factors (GEFs) facilitate the exchange of GDP with GTP and thereby turn ROPs into a signalling-activated ROP-GTP state. Plants possess a unique class of GEFs harbouring a plant specific ROP nucleotide exchanger domain (PRONE). We performed phylogenetic analyses and annotated barley PRONE GEFs. HvGEF14 is expressed in leaf epidermal tissue and downregulated after inoculation with Blumeria graminis f.sp. hordei. Protein-protein interaction assays indicate that HvGEF14 and the type I barley ROP protein HvRACB can interact in yeast and in planta. Overexpression of HvGEF14 further recruited the ROP-GTP downstream interactor HvRIC171 to the cell periphery and let to interaction of HvRACB with an extended CRIB (Cdc42/Rac Interactive Binding motif) peptide of HvRIC171 in a similar manner as constitutively activated HvRACB. Finally, the over expression of HvGEF14 led to enhanced susceptibility to fungal entry while HvGEF14 RNAi provoked a trend to more penetration resistance. HvGEF14 might therefore play a role in the activation of HvRACB in barley epidermal cells, which is crucial for fungal penetration success.

scholarly journals Multiple Invasions of Visitor, a DD41D Family of Tc1/mariner Transposons, throughout the Evolution of Vertebrates

2020 ◽  
Vol 12 (7) ◽  
pp. 1060-1073 ◽  
Author(s):  
Dan Shen ◽  
Bo Gao ◽  
Csaba Miskey ◽  
Cai Chen ◽  
Yatong Sang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Horizontal Transfer ◽  
Phylogenetic Analyses ◽  
Land Plant ◽  
Activity Assay ◽  
Animal Kingdom ◽  
Close Relationship ◽  
Recombination Activating Gene ◽  
Multiple Invasions ◽  
Relationship Of

Abstract Although the DD41D (named as Visitor, VS) family of Tc1/mariner transposons was discovered in Arthropods and Mollusca, the evolution profile of this family is still largely unknown. We found that VS is widespread in the animal kingdom, including 140 species of 18 orders in invertebrates and 30 species of 12 orders in vertebrates, and one land plant species. Our data revealed multiple horizontal transfer events in both invertebrates and vertebrates and invasion into multiple lineages of mammals, including Chiroptera (seven species), Dasyuromorphia/Marsupialia (one species), Didelphimorphia/Marsupialia (one species), Diprotodontia/Marsupialia (two species), and Primates (one species). Phylogenetic analysis revealed a close relationship of VSs to DD37D/maT and DD34D/mariner and confirmed that VSs with the DD40D signature identified previously are not a distinct family but originated from DD41D/VS. Age analysis revealed that the most recent invasion of VSs was found in ray-finned fishes and a toad, followed by relatively young invasions in bats and marsupials, whereas VSs in mammals, jawless fishes, and lizards were mainly represented by ancient copies, suggesting old age. Phylogenetic analyses and comparison of pairwise distances between VSs and recombination-activating gene 1 (RAG1) support horizontal transfer events of VSs in vertebrates. The intact VSs from bats were nonfunctional as determined by the transposition activity assay. Some vertebrate lineages and species were identified as the hot hosts of Tc1/mariner transposons. Overall, our study presents the evolution profile of VSs and suggests that VSs play roles in diversifying and shaping the genomes of diverse animal lineages.

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