scholarly journals Abundantly expressed class of non-coding RNAs conserved through the multicellular evolution of dictyostelid social amoebae

2020 ◽  
Author(s):  
Jonas Kjellin ◽  
Lotta Avesson ◽  
Johan Reimegård ◽  
Zhen Liao ◽  
Ludwig Eichinger ◽  
...  
Keyword(s):  
Current Knowledge ◽  
Great Majority ◽  
Class I ◽  
Last Common Ancestor ◽  
Sequence Motifs ◽  
Multicellular Development ◽  
Search Approach ◽  
Diverse Groups ◽  
Rna Genes ◽  
Social Amoebae

AbstractBackgroundAggregative multicellularity has evolved multiple times in diverse groups of eukaryotes. One of the most well-studied examples is the development of dictyostelid social amoebae, e.g. Dictyostelium discoideum. However, it is still poorly understood why multicellularity emerged in these amoebae while the great majority of other members of Amoebozoa are unicellular. Previously a novel type of non-coding RNA, Class I RNAs, was identified in D. discoideum and demonstrated to be important for normal multicellular development. In this study we investigated Class I RNA evolution and its connection to multicellular development.ResultsNew Class I RNA genes were identified by constructing a co-variance model combined with a scoring system based on conserved up-stream sequences. Multiple genes were predicted in representatives of each major group of Dictyostelia and expression analysis validated that our search approach can identify expressed Class I RNA genes with high accuracy and sensitivity. Further studies showed that Class I RNAs are ubiquitous in Dictyostelia and share several highly conserved structure and sequence motifs. Class I RNA genes appear to be unique to dictyostelid social amoebae since they could not be identified in searches in outgroup genomes, including the closest known relatives to Dictyostelia.ConclusionOur results show that Class I RNA is an ancient abundant class of ncRNAs, likely to have been present in the last common ancestor of Dictyostelia dating back at least 600 million years. Taken together, our current knowledge of Class I RNAs suggests that they may have been involved in evolution of multicellularity in Dictyostelia.

scholarly journals Discovery of an ancient MHC category with both class I and class II features

2021 ◽  
Vol 118 (51) ◽  
pp. e2108104118
Author(s):  
Kazuhiko Okamura ◽  
Johannes M. Dijkstra ◽  
Kentaro Tsukamoto ◽  
Unni Grimholt ◽  
Geert F. Wiegertjes ◽  
...  
Keyword(s):  
Mhc Class I ◽  
Class Ii ◽  
Class I ◽  
Sequence Motifs ◽  
Critical Question ◽  
Specific Sequence ◽  
Mhc Molecules ◽  
Mhc Class I Molecule ◽  
Chain Organization ◽  
Lymphocyte Populations

Two classes of major histocompatibility complex (MHC) molecules, MHC class I and class II, play important roles in our immune system, presenting antigens to functionally distinct T lymphocyte populations. However, the origin of this essential MHC class divergence is poorly understood. Here, we discovered a category of MHC molecules (W-category) in the most primitive jawed vertebrates, cartilaginous fish, and also in bony fish and tetrapods. W-category, surprisingly, possesses class II–type α- and β-chain organization together with class I–specific sequence motifs for interdomain binding, and the W-category α2 domain shows unprecedented, phylogenetic similarity with β2-microglobulin of class I. Based on the results, we propose a model in which the ancestral MHC class I molecule evolved from class II–type W-category. The discovery of the ancient MHC group, W-category, sheds a light on the long-standing critical question of the MHC class divergence and suggests that class II type came first.

Early Molecular Evolution

2006 ◽  
Vol 52 (3-4) ◽  
pp. 375-387 ◽  
Author(s):  
Edward N. Trifonov
Keyword(s):  
Molecular Evolution ◽  
Protein Sequence ◽  
Last Common Ancestor ◽  
Sequence Motifs ◽  
Molecular Events ◽  
Function Modules ◽  
Recent Developments ◽  
Module Size ◽  
Protein Sequence Motifs ◽  
Polypeptide Chains

Four fundamentally novel, recent developments make a basis for the Theory of Early Molecular Evolution. The theory outlines the molecular events from the onset of the triplet code to the formation of the earliest sequence/structure/function modules of proteins. These developments are: (1) Reconstruction of the evolutionary chart of codons; (2) Discovery of omnipresent protein sequence motifs, apparently conserved since the last common ancestor; (3) Discovery of closed loops—standard structural modules of modern proteins; (4) Construction of protein sequence space of module size fragments, with far-reaching evolutionary implications. The theory generates numerous predictions, confirmed by massive nucleotide and protein sequence analyses, such as existence of two distinct classes of amino acids, and their periodical distribution along the sequences. The emerging picture of the earliest molecular evolutionary events is outlined: consecutive engagement of codons, formation of the earliest short peptides, and growth of the polypeptide chains to the size of loop closure, 25-30 residues.

scholarly journals Wild Dictyostelium discoideum social amoebae show plastic responses to the presence of nonrelatives during multicellular development

2020 ◽  
Vol 10 (3) ◽  
pp. 1119-1134
Author(s):  
Suegene Noh ◽  
Lauren Christopher ◽  
Joan E. Strassmann ◽  
David C. Queller
Keyword(s):  
Dictyostelium Discoideum ◽  
Multicellular Development ◽  
Plastic Responses ◽  
Social Amoebae

Various dictyostelids from the environment can produce multilamellar bodies

2020 ◽  
Vol 66 (12) ◽  
pp. 679-688
Author(s):  
Alicia F. Durocher ◽  
Cynthia Gagné-Thivierge ◽  
Steve J. Charette
Keyword(s):  
Cell Communication ◽  
Laboratory Strain ◽  
Food Storage ◽  
Epifluorescence Microscopy ◽  
Free Living ◽  
Multicellular Development ◽  
Multilamellar Bodies ◽  
Transmission Electron ◽  
Axenic Conditions ◽  
Social Amoebae

Multilamellar bodies (MLBs), structures composed of concentric membrane layers, are known to be produced by different protozoa, including species of ciliates, free-living amoebae, and Dictyostelium discoideum social amoebae. Initially believed to be metabolic waste, potential roles like cell communication and food storage have been suggested for D. discoideum MLBs, which could be useful for the multicellular development of social amoebae and as a food source. However, among dictyostelids, this phenomenon has only been observed with D. discoideum, and mainly with laboratory strains grown in axenic conditions. It was thought that other social amoebae may also produce MLBs. Four environmental social amoeba isolates were characterized. All strains belong to the Dictyostelium genus, including some likely to be Dictyostelium giganteum. They have distinctive phenotypes comprising their growth rate on Klebsiella aerogenes lawns and the morphology of their fruiting bodies. They all produce MLBs like those produced by a D. discoideum laboratory strain when grown on K. aerogenes lawns, as revealed by analysis using the H36 antibody in epifluorescence microscopy as well as by transmission electron microscopy. Consequently, this study shows that MLBs are produced by various dictyostelid species, which further supports a role for MLBs in the lifestyle of amoebae.

scholarly journals Self-peptide released from class II HLA-DR1 exhibits a hydrophobic two-residue contact motif.

1992 ◽  
Vol 175 (6) ◽  
pp. 1799-1803 ◽  
Author(s):  
H Kropshofer ◽  
H Max ◽  
C A Müller ◽  
F Hesse ◽  
S Stevanovic ◽  
...  
Keyword(s):  
T Cell ◽  
Cell Receptor ◽  
Class Ii ◽  
Peptide Sequence ◽  
Class I ◽  
T Cell Epitopes ◽  
Sequence Motifs ◽  
Peptide Fragments ◽  
Residue Contact ◽  
High Affinity

Peptide fragments of foreign and self-proteins are of great immunologic importance as their binding to major histocompatibility complex (MHC) class I or II molecules makes an interaction with a corresponding T cell receptor possible. Recently, allele-specific peptide sequence motifs proved to be responsible for MHC binding, no matter whether self- or non-self-antigens were involved. Up to now, all investigated human class II-associated peptides were derived from foreign antigenic proteins. Therefore, we undertook sequence and binding analyses with a 16-mer self-peptide (SP3) that has been eluted from HLA-DR1. Here we demonstrate, by synthetic polyalanine-based 13-mer analogues of SP3, that two bulky hydrophobic anchor residues with relative spacing i, i + 8 are sufficient for high affinity binding. This is consistent with the hydrophobic i, i + 8 binding pattern recently found for DR-restricted T cell epitopes. Nevertheless, highly helical alanine-based design peptides with anchor spacing i, i + 9 exhibit maximal affinity, whereas replacement of alanine by helix destabilizing proline abrogates binding. Thus, a two-residue contact motif is the common minimal requirement of self- and foreign peptides for high affinity anchoring to HLA-DR1. In contrast to class I, the anchor spacing of DR1-associated peptides seems to bear some variability due to conformational diversity.

scholarly journals Synergistic Effects of Toxic Elements on Heat Shock Proteins

2014 ◽  
Vol 2014 ◽  
pp. 1-17 ◽  
Author(s):  
Khalid Mahmood ◽  
Saima Jadoon ◽  
Qaisar Mahmood ◽  
Muhammad Irshad ◽  
Jamshaid Hussain
Keyword(s):  
Heat Shock ◽  
Heat Shock Proteins ◽  
Toxic Elements ◽  
Current Knowledge ◽  
Synergistic Effects ◽  
Expression Patterns ◽  
Expression Levels ◽  
Functional Capabilities ◽  
Shock Proteins ◽  
Diverse Groups

Heat shock proteins show remarkable variations in their expression levels under a variety of toxic conditions. A research span expanded over five decades has revealed their molecular characterization, gene regulation, expression patterns, vast similarity in diverse groups, and broad range of functional capabilities. Their functions include protection and tolerance against cytotoxic conditions through their molecular chaperoning activity, maintaining cytoskeleton stability, and assisting in cell signaling. However, their role as biomarkers for monitoring the environmental risk assessment is controversial due to a number of conflicting, validating, and nonvalidating reports. The current knowledge regarding the interpretation of HSPs expression levels has been discussed in the present review. The candidature of heat shock proteins as biomarkers of toxicity is thus far unreliable due to synergistic effects of toxicants and other environmental factors. The adoption of heat shock proteins as “suit of biomarkers in a set of organisms” requires further investigation.

scholarly journals Neonatal Fc receptor (FcRn) – not only transporter of maternal IgG

2018 ◽  
Vol 72 ◽  
pp. 701-727
Author(s):  
Joanna E. Mikulska
Keyword(s):  
Mhc Class I ◽  
Current Knowledge ◽  
Cell Types ◽  
Fc Receptor ◽  
Class I ◽  
Neonatal Fc Receptor ◽  
The Status ◽  
And Function ◽  
Different Cell Types ◽  
Maternal Igg

The neonatal Fc receptor, (FcRn) is a transmembrane, heterodimeric glycoprotein with a structure similar to MHC class I molecules. In contrast to MHC class I antigens, FcRn does not bind to peptides (antigens) but interacts with the Fc fragment of IgG and albumin. The FcRn-IgG interaction as well as the FcRn-albumin interaction occur at acidic pH (optimally at pH 5.0-6.5) but not in physiological environment. These two ligands bind to distinct binding sites on the receptor molecule and by different mechanisms. Now, it is known that the expression of FcRn is not restricted to sites involved in the transport of maternal IgG, and this receptor is not responsible only for transfer the passive immunity from mother to the offspring. But FcRn has a much broader range of expression and function, throughout life and in many different cell types and tissues of humans and animals. This review summarizes the status of our knowledge on the expression, interaction with ligands and functions of the neonatal Fc receptor. This article shows also the possibilities of utilizing a current knowledge on FcRn for therapeutic purposes.

scholarly journals Terpene synthase genes in eukaryotes beyond plants and fungi: Occurrence in social amoebae

2016 ◽  
Vol 113 (43) ◽  
pp. 12132-12137 ◽  
Author(s):  
Xinlu Chen ◽  
Tobias G. Köllner ◽  
Qidong Jia ◽  
Ayla Norris ◽  
Balaji Santhanam ◽  
...  
Keyword(s):  
Early Stage ◽  
Terpene Synthase ◽  
Functional Study ◽  
Terpene Biosynthesis ◽  
Terpene Synthases ◽  
Multicellular Development ◽  
Stage Of Development ◽  
The Social ◽  
Volatile Terpenes ◽  
Social Amoebae

Terpenes are structurally diverse natural products involved in many ecological interactions. The pivotal enzymes for terpene biosynthesis, terpene synthases (TPSs), had been described only in plants and fungi in the eukaryotic domain. In this report, we systematically analyzed the genome sequences of a broad range of nonplant/nonfungus eukaryotes and identified putative TPS genes in six species of amoebae, five of which are multicellular social amoebae from the order of Dictyosteliida. A phylogenetic analysis revealed that amoebal TPSs are evolutionarily more closely related to fungal TPSs than to bacterial TPSs. The social amoeba Dictyostelium discoideum was selected for functional study of the identified TPSs. D. discoideum grows as a unicellular organism when food is abundant and switches from vegetative growth to multicellular development upon starvation. We found that expression of most D. discoideum TPS genes was induced during development. Upon heterologous expression, all nine TPSs from D. discoideum showed sesquiterpene synthase activities. Some also exhibited monoterpene and/or diterpene synthase activities. Direct measurement of volatile terpenes in cultures of D. discoideum revealed essentially no emission at an early stage of development. In contrast, a bouquet of terpenes, dominated by sesquiterpenes including β-barbatene and (E,E)-α-farnesene, was detected at the middle and late stages of development, suggesting a development-specific function of volatile terpenes in D. discoideum. The patchy distribution of TPS genes in the eukaryotic domain and the evidence for TPS function in D. discoideum indicate that the TPS genes mediate lineage-specific adaptations.

scholarly journals Relevance of Polymorphic KIR and HLA Class I Genes in NK-Cell-Based Immunotherapies for Adult Leukemic Patients

Cancers ◽  
2021 ◽  
Vol 13 (15) ◽  
pp. 3767
Author(s):  
Léa Dubreuil ◽  
Patrice Chevallier ◽  
Christelle Retière ◽  
Katia Gagne
Keyword(s):  
Nk Cells ◽  
Nk Cell ◽  
Current Knowledge ◽  
Killer Cell ◽  
Hla Class I ◽  
Class I ◽  
Cell Repertoire ◽  
Hematopoietic Stem ◽  
Structural Formation ◽  
The Impact

Since the mid-1990s, the biology and functions of natural killer (NK) cells have been deeply investigated in healthy individuals and in people with diseases. These effector cells play a particularly crucial role after allogeneic hematopoietic stem-cell transplantation (HSCT) through their graft-versus-leukemia (GvL) effect, which is mainly mediated through polymorphic killer-cell immunoglobulin-like receptors (KIRs) and their cognates, HLA class I ligands. In this review, we present how KIRs and HLA class I ligands modulate the structural formation and the functional education of NK cells. In particular, we decipher the current knowledge about the extent of KIR and HLA class I gene polymorphisms, as well as their expression, interaction, and functional impact on the KIR+ NK cell repertoire in a physiological context and in a leukemic context. In addition, we present the impact of NK cell alloreactivity on the outcomes of HSCT in adult patients with acute leukemia, as well as a description of genetic models of KIRs and NK cell reconstitution, with a focus on emergent T-cell-repleted haplo-identical HSCT using cyclosphosphamide post-grafting (haplo-PTCy). Then, we document how the immunogenetics of KIR/HLA and the immunobiology of NK cells could improve the relapse incidence after haplo-PTCy. Ultimately, we review the emerging NK-cell-based immunotherapies for leukemic patients in addition to HSCT.

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