Slipknotted and unknotted monovalent cation-proton antiporters evolved from a common ancestor

While the slipknot topology in proteins has been known for over a decade, its evolutionary origin is still a mystery. We have identified a previously overlooked slipknot motif in a family of two-domain membrane transporters. Moreover, we found that these proteins are homologous to several families of unknotted membrane proteins. This allows us to directly investigate the evolution of the slipknot motif. Based on our comprehensive analysis of 17 distantly related protein families, we have found that slipknotted and unknotted proteins share a common structural motif. Furthermore, this motif is conserved on the sequential level as well. Our results suggest that, regardless of topology, the proteins we studied evolved from a common unknotted ancestor single domain protein. Our phylogenetic analysis suggests the presence of at least seven parallel evolutionary scenarios that led to the current diversity of proteins in question. The tools we have developed in the process can now be used to investigate the evolution of other repeated-domain proteins.

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The Speed of Allosteric Signaling Within a Single-Domain Protein

The Journal of Physical Chemistry Letters ◽

10.1021/acs.jpclett.1c00915 ◽

2021 ◽

pp. 4262-4267

Author(s):

Olga Bozovic ◽

Jeannette Ruf ◽

Claudio Zanobini ◽

Brankica Jankovic ◽

David Buhrke ◽

...

Keyword(s):

Single Domain ◽

Single Domain Protein ◽

Domain Protein

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Low Force Unfolding of a Single-Domain Protein by Parallel Pathways

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.0c11308 ◽

2021 ◽

Vol 125 (7) ◽

pp. 1799-1805

Author(s):

Pavel I. Zhuravlev ◽

Michael Hinczewski ◽

D. Thirumalai

Keyword(s):

Single Domain ◽

Single Domain Protein ◽

Parallel Pathways ◽

Domain Protein

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Isolation and Phylogenetic Analysis of Novel Viruses Infecting the Phytoplankton Phaeocystis globosa (Prymnesiophyceae)

Applied and Environmental Microbiology ◽

10.1128/aem.70.6.3700-3705.2004 ◽

2004 ◽

Vol 70 (6) ◽

pp. 3700-3705 ◽

Cited By ~ 53

Author(s):

C. P. D. Brussaard ◽

S. M. Short ◽

C. M. Frederickson ◽

C. A. Suttle

Keyword(s):

Phylogenetic Analysis ◽

Dna Polymerase ◽

Coastal Waters ◽

Common Ancestor ◽

Genetic Relatedness ◽

Amino Acid Sequences ◽

Polymerase Gene ◽

Phaeocystis Globosa ◽

The Family ◽

Algal Host

ABSTRACT Viruses infecting the harmful bloom-causing alga Phaeocystis globosa (Prymnesiophyceae) were readily isolated from Dutch coastal waters (southern North Sea) in 2000 and 2001. Our data show a large increase in the abundance of putative P. globosa viruses during blooms of P. globosa, suggesting that viruses are an important source of mortality for this alga. In order to examine genetic relatedness among viruses infecting P. globosa and other phytoplankton, DNA polymerase gene (pol) fragments were amplified and the inferred amino acid sequences were phylogenetically analyzed. The results demonstrated that viruses infecting P. globosa formed a closely related monophyletic group within the family Phycodnaviridae, with at least 96.9% similarity to each other. The sequences grouped most closely with others from viruses that infect the prymnesiophyte algae Chrysochromulina brevifilum and Chrysochromulina strobilus. Whether the P. globosa viruses belong to the genus Prymnesiovirus or form a separate group needs further study. Our data suggest that, like their phytoplankton hosts, the Chrysochromulina and Phaeocystis viruses share a common ancestor and that these prymnesioviruses and their algal host have coevolved.

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Functional evolution of nuclear structure

The Journal of Cell Biology ◽

10.1083/jcb.201103171 ◽

2011 ◽

Vol 195 (2) ◽

pp. 171-181 ◽

Cited By ~ 70

Author(s):

Katherine L. Wilson ◽

Scott C. Dawson

Keyword(s):

Membrane Proteins ◽

Nuclear Structure ◽

Common Ancestor ◽

Nuclear Pore ◽

Nuclear Pore Complexes ◽

Chromatin Binding ◽

Endomembrane System ◽

Tightly Coupled ◽

Pore Complexes ◽

Eukaryotic Supergroup

The evolution of the nucleus, the defining feature of eukaryotic cells, was long shrouded in speculation and mystery. There is now strong evidence that nuclear pore complexes (NPCs) and nuclear membranes coevolved with the endomembrane system, and that the last eukaryotic common ancestor (LECA) had fully functional NPCs. Recent studies have identified many components of the nuclear envelope in living Opisthokonts, the eukaryotic supergroup that includes fungi and metazoan animals. These components include diverse chromatin-binding membrane proteins, and membrane proteins with adhesive lumenal domains that may have contributed to the evolution of nuclear membrane architecture. Further discoveries about the nucleoskeleton suggest that the evolution of nuclear structure was tightly coupled to genome partitioning during mitosis.

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Bacterial ß-Barrel Outer Membrane Proteins

Handbook of Research on Systems Biology Applications in Medicine ◽

10.4018/978-1-60566-076-9.ch010 ◽

2009 ◽

pp. 182-207

Author(s):

Pantelis G. Bagos ◽

Stavros J. Hamodrakas

Keyword(s):

Membrane Proteins ◽

Outer Membrane ◽

Bacterial Cell ◽

Outer Membrane Proteins ◽

Structural Features ◽

Structure And Function ◽

Structural Motif ◽

Functional Roles ◽

Bacterial Outer Membrane ◽

And Function

ß-barrel outer membrane proteins constitute the second and less well-studied class of transmembrane proteins. They are present exclusively in the outer membrane of Gram-negative bacteria and presumably in the outer membrane of mitochondria and chloroplasts. During the last few years, remarkable advances have been made towards an understanding of their functional and structural features. It is now wellknown that ß-barrels are performing a large variety of biologically important functions for the bacterial cell. Such functions include acting as specific or non-specific channels, receptors for various compounds, enzymes, translocation channels, structural proteins, and adhesion proteins. All these functional roles are of great importance for the survival of the bacterial cell under various environmental conditions or for the pathogenic properties expressed by these organisms. This chapter reviews the currently available literature regarding the structure and function of bacterial outer membrane proteins. We emphasize the functional diversity expressed by a common structural motif such as the ß-barrel, and we provide evidence from the current literature for dozens of newly discovered families of transmembrane ß-barrels.

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Platypus immunoglobulin M and the divergence of the two extant monotreme lineages

Australian Mammalogy ◽

10.1071/am03087 ◽

2003 ◽

Vol 25 (1) ◽

pp. 87 ◽

Cited By ~ 8

Author(s):

K Belov ◽

L Hellman

Keyword(s):

Phylogenetic Analysis ◽

Amino Acid ◽

Common Ancestor ◽

Variable Region ◽

Immunoglobulin M ◽

Last Common Ancestor ◽

Constant Region ◽

Sequence Comparisons ◽

Level Sequence ◽

High Level

A full-length cDNA clone encoding the platypus (Ornithorynchus anatinus) immunoglobulin M (IgM) heavy chain was isolated from a spleen cDNA library using a short-beaked echidna (Tachyglossus aculeatus) IgM constant region (Cµ) probe. The isolation of platypus IgM shows that O. anatinus, like all other examined jawed vertebrates, express a classical IgM molecule. Amino acid sequence comparisons of the constant regions of IgM reveals a high level sequence conservation between O. anatinus and T. aculeatus sequences (87%), and only approximately 48% identity between O. anatinus and therian Cµ sequences. The variable region of this clone belongs to clan 3, supporting the view that this family is used preferentially, if not exclusively by O. anatinus, as opposed to the use of all three variable region clans by T. aculeatus. Phylogenetic analysis of Cµ sequences supports the traditional Theria hypothesis and suggests that the O. anatinus and T. aculeatus lineages separated from their last common ancestor approximately 21 million years ago.

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Morphology-based phylogenetic analysis of the treehopper tribe Smiliini (Hemiptera: Membracidae: Smiliinae), with reinstatement of the tribe Telamonini

Zootaxa ◽

10.11646/zootaxa.3047.1.1 ◽

2011 ◽

Vol 3047 (1) ◽

pp. 1 ◽

Cited By ~ 6

Author(s):

MATTHEW S. WALLACE

Keyword(s):

Phylogenetic Analysis ◽

Common Ancestor ◽

Hind Wing ◽

Morphological Characters ◽

Dorsal Margin ◽

Incertae Sedis ◽

Plant Associations ◽

Original Dataset ◽

The Common ◽

Morphological Differences

Members of the Smiliini, the nominotypical tribe of the large New World subfamily Smiliinae, are predominately Nearctic in distribution. This tribe included 169 mostly tree-feeding species in 23 genera. A parsimony-based phylogenetic analysis of an original dataset comprising 89 traditional and newly discovered morphological characters for 69 species, including representatives of 22 of the 23 described genera of Smiliini and five other previously recognized tribes of the subfamily, resulted in a single most parsimonious tree with three major clades. The broad recent concept of Smiliini (including Telamonini as a junior synonym) was not recovered as monophyletic by the analysis. Instead, the analysis supported narrower definitions of both Telamonini, here reinstated from synonymy, and Smiliini. A key and diagnoses are given to define these tribes, along with discussions of their phylogeny, biogeography, and host plant associations. The genera Antianthe Fowler, Hemicardiacus Plummer, Smilirhexia McKamey, and Tropidarnis Fowler are placed as Smiliinae, incertae sedis. Based on the phylogeny, several genera from both tribes including Atymna Stål, Cyrtolobus Goding, Heliria Stål, and Telamona Fitch are not monophyletic. Diagnostic characters emphasizing the morphological differences between the Smiliini and Telamonini include the dorsal margin of the head, the shape of the pronotum, the size of the pronotal humeral angles, the presence or absence of pronotal longitudinal rugae, the size of forewing cells, variations in the fusion of veins R and M apically in both the foreand hind wing, and the shape of the apex of the female second valvulae. Mapping geographic distribution onto the phylogeny suggests that the common ancestor of the ingroup (all three clades) occurred in Central America and Mexico, with multiple dispersals to temperate North America. Many Smiliini and Telamonini feed on various species of oak (Quercus) and the close evolutionary association between these insects and their hosts is discussed.

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