Protein families in the metazoan genome

Development ◽  
1994 ◽  
Vol 1994 (Supplement) ◽  
pp. 27-33 ◽  
Author(s):  
Cyrus Chothia
Keyword(s):  
Conformational Changes ◽  
Evolution Of Development ◽  
Gene Duplications ◽  
Protein Families ◽  
And Function ◽  
Multicellular Organisms ◽  
Related Proteins ◽  
Initial Results ◽  
Genome Projects ◽  
Data Banks

The evolution of development involves the development of new proteins. Estimates based on the initial results of the genome projects, and on the data banks of protein sequences and structures, suggest that the large majority of proteins come from no more than one thousand families. Members of a family are descended from a common ancestor. Protein families evolve by gene duplication and mutation. Mutations change the conformation of the peripheral regions of proteins; i.e. the regions that are involved, at least in part, in their function. If mutations proceed until only 20% of the residues in related proteins are identical, it is common for the conformational changes to affect half the structure. Most of the proteins involved in the interactions of cells, and in their assembly to form multicellular organisms, are mosaic proteins. These are large and have a modular structure, in that they are built of sets of homologous domains that are drawn from a relatively small number of protein families. Patthy's model for the evolution of mosaic proteins describes how they arose through the insertion of introns into genes, gene duplications and intronic recombination. The rates of progress in the genome sequencing projects, and in protein structure analyses, means that in a few years we will have a fairly complete outline description of the molecules responsible for the structure and function of organisms at several different levels of developmental complexity. This should make a major contribution to our understanding of the evolution of development.

scholarly journals Structural insights into assembly and function of the RSC chromatin remodeling complex

2020 ◽  
Author(s):  
Richard W. Baker ◽  
Janice M. Reimer ◽  
Peter J. Carman ◽  
Tsutomu Arakawa ◽  
Roberto Dominguez ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Structural Data ◽  
Underlying Mechanism ◽  
Specific Protein ◽  
Helical Conformation ◽  
Chromatin Remodelers ◽  
Rsc Complex ◽  
And Function ◽  
Related Proteins ◽  
Structural Insights

AbstractChromatin remodelers regulate the position and composition of nucleosomes throughout the genome, producing different remodeling outcomes despite a shared underlying mechanism based on a conserved RecA DNA translocase. How this functional diversity is achieved remains unknown despite recent cryo-electron microscopy (cryo-EM) reconstructions of several remodelers, including the yeast RSC complex. To address this, we have focused on a RSC subcomplex comprising its ATPase (Sth1), the essential actin-related proteins (ARPs) Arp7 and Arp9, and the fungal-specific protein Rtt102. Combining cryo-EM and biochemistry of this subcomplex, which exhibits regulation of remodeling by the ARPs, we show that ARP binding induces a helical conformation in the HSA domain of Sth1, which bridges the ATPase domain with the bulk of the complex. Surprisingly, the ARP module is rotated by 120° in the subcomplex relative to full RSC about a pivot point previously identified as a regulatory hub in Sth1, suggesting that large conformational changes are part of Sth1 regulation and RSC assembly. We also show that an interaction between Sth1 and the nucleosome acidic patch, which appears to be conserved among SWI/SNF remodelers, enhances remodeling. Taken together, our structural data shed light on the assembly and function of the RSC complex.

Influence of Ascorbic Acid on the Structure and Function of Alpha-2- macroglobulin: Investigations using Spectroscopic and Thermodynamic Techniques

2020 ◽  
Vol 27 (3) ◽  
pp. 201-209
Author(s):  
Syed Saqib Ali ◽  
Mohammad Khalid Zia ◽  
Tooba Siddiqui ◽  
Haseeb Ahsan ◽  
Fahim Halim Khan
Keyword(s):  
Ascorbic Acid ◽  
Conformational Changes ◽  
Structural Changes ◽  
The Body ◽  
Titration Calorimetry ◽  
Spectroscopic Techniques ◽  
Human Beings ◽  
Plasma Ascorbic Acid ◽  
Dietary Antioxidant ◽  
And Function

Background: Ascorbic acid is a classic dietary antioxidant which plays an important role in the body of human beings. It is commonly found in various foods as well as taken as dietary supplement. Objective: The plasma ascorbic acid concentration may range from low, as in chronic or acute oxidative stress to high if delivered intravenously during cancer treatment. Sheep alpha-2- macroglobulin (α2M), a human α2M homologue is a large tetrameric glycoprotein of 630 kDa with antiproteinase activity, found in sheep’s blood. Methods: In the present study, the interaction of ascorbic acid with alpha-2-macroglobulin was explored in the presence of visible light by utilizing various spectroscopic techniques and isothermal titration calorimetry (ITC). Results: UV-vis and fluorescence spectroscopy suggests the formation of a complex between ascorbic acid and α2M apparent by increased absorbance and decreased fluorescence. Secondary structural changes in the α2M were investigated by CD and FT-IR spectroscopy. Our findings suggest the induction of subtle conformational changes in α2M induced by ascorbic acid. Thermodynamics signatures of ascorbic acid and α2M interaction indicate that the binding is an enthalpy-driven process. Conclusion: It is possible that ascorbic acid binds and compromises antiproteinase activity of α2M by inducing changes in the secondary structure of the protein.

scholarly journals Effects of Dysbiosis and Dietary Manipulation on the Digestive Microbiota of a Detritivorous Arthropod

2021 ◽  
Vol 9 (1) ◽  
pp. 148
Author(s):  
Marius Bredon ◽  
Elisabeth Depuydt ◽  
Lucas Brisson ◽  
Laurent Moulin ◽  
Ciriac Charles ◽  
...  
Keyword(s):  
Crucial Role ◽  
Structure And Function ◽  
Ecological Interactions ◽  
Dietary Manipulation ◽  
Biotic Factors ◽  
Abiotic And Biotic Factors ◽  
And Function ◽  
Multicellular Organisms ◽  
Over Time

The crucial role of microbes in the evolution, development, health, and ecological interactions of multicellular organisms is now widely recognized in the holobiont concept. However, the structure and stability of microbiota are highly dependent on abiotic and biotic factors, especially in the gut, which can be colonized by transient bacteria depending on the host’s diet. We studied these impacts by manipulating the digestive microbiota of the detritivore Armadillidium vulgare and analyzing the consequences on its structure and function. Hosts were exposed to initial starvation and then were fed diets that varied the different components of lignocellulose. A total of 72 digestive microbiota were analyzed according to the type of the diet (standard or enriched in cellulose, lignin, or hemicellulose) and the period following dysbiosis. The results showed that microbiota from the hepatopancreas were very stable and resilient, while the most diverse and labile over time were found in the hindgut. Dysbiosis and selective diets may have affected the host fitness by altering the structure of the microbiota and its predicted functions. Overall, these modifications can therefore have effects not only on the holobiont, but also on the “eco-holobiont” conceptualization of macroorganisms.

scholarly journals The Autophagy Machinery in Human-Parasitic Protists; Diverse Functions for Universally Conserved Proteins

Cells ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1258
Author(s):  
Hirokazu Sakamoto ◽  
Kumiko Nakada-Tsukui ◽  
Sébastien Besteiro
Keyword(s):  
Membrane Vesicle ◽  
Model Organisms ◽  
Unicellular Eukaryotes ◽  
Current State ◽  
Important Challenge ◽  
Molecular Machinery ◽  
Cellular Machinery ◽  
Apparent Reduction ◽  
Related Proteins ◽  
Genome Projects

Autophagy is a eukaryotic cellular machinery that is able to degrade large intracellular components, including organelles, and plays a pivotal role in cellular homeostasis. Target materials are enclosed by a double membrane vesicle called autophagosome, whose formation is coordinated by autophagy-related proteins (ATGs). Studies of yeast and Metazoa have identified approximately 40 ATGs. Genome projects for unicellular eukaryotes revealed that some ATGs are conserved in all eukaryotic supergroups but others have arisen or were lost during evolution in some specific lineages. In spite of an apparent reduction in the ATG molecular machinery found in parasitic protists, it has become clear that ATGs play an important role in stage differentiation or organelle maintenance, sometimes with an original function that is unrelated to canonical degradative autophagy. In this review, we aim to briefly summarize the current state of knowledge in parasitic protists, in the light of the latest important findings from more canonical model organisms. Determining the roles of ATGs and the diversity of their functions in various lineages is an important challenge for understanding the evolutionary background of autophagy.

scholarly journals Evolution of the hedgehog Gene Family

Genetics ◽  
1996 ◽  
Vol 142 (3) ◽  
pp. 965-972 ◽  
Author(s):  
Sudhir Kumar ◽  
Kristi A Balczarek ◽  
Zhi-Chun Lai
Keyword(s):  
Intercellular Communication ◽  
Short Range ◽  
Gene Duplications ◽  
Future Directions ◽  
Amino Terminal ◽  
Terminal Fragment ◽  
Carboxyl Terminal ◽  
Multicellular Organisms ◽  
Amino Terminal Fragment

Abstract Effective intercellular communication is an important feature in the development of multicellular organisms. Secreted hedgehog (hh) protein is essential for both long- and short-range cellular signaling required for body pattern formation in animals. In a molecular evolutionary study, we find that the vertebrate homologs of the Drosophila hh gene arose by two gene duplications: the first gave rise to Desert hh, whereas the second produced the Indian and Sonic hh genes. Both duplications occurred before the emergence of vertebrates and probably before the evolution of chordates. The amino-terminal fragment of the hh precursor, crucial in long- and short-range intercellular communication, evolves two to four times slower than the carboxyl-terminal fragment in both Drosophila hh and its vertebrate homologues, suggesting conservation of mechanism of hh action in animals. A majority of amino acid substitutions in the amino- and carboxyl-terminal fragments are conservative, but the carboxyl-terminal domain has undergone extensive insertion-deletion events while maintaining its autocleavage protease activity. Our results point to similarity of evolutionary constraints among sites of Drosophila and vertebrate hh homologs and suggest some future directions for understanding the role of hh genes in the evolution of developmental complexity in animals.

scholarly journals Developing a vocabulary and ontology for modeling insect natural history data: example data, use cases, and competency questions

2019 ◽  
Vol 7 ◽  
Author(s):  
Brian Stucky ◽  
James Balhoff ◽  
Narayani Barve ◽  
Vijay Barve ◽  
Laura Brenskelle ◽  
...  
Keyword(s):  
Natural History ◽  
Large Scale ◽  
Use Cases ◽  
Data Systems ◽  
Multiple Sources ◽  
History Data ◽  
Insect Ecology ◽  
Many Sources ◽  
Multicellular Organisms ◽  
Initial Results

Insects are possibly the most taxonomically and ecologically diverse class of multicellular organisms on Earth. Consequently, they provide nearly unlimited opportunities to develop and test ecological and evolutionary hypotheses. Currently, however, large-scale studies of insect ecology, behavior, and trait evolution are impeded by the difficulty in obtaining and analyzing data derived from natural history observations of insects. These data are typically highly heterogeneous and widely scattered among many sources, which makes developing robust information systems to aggregate and disseminate them a significant challenge. As a step towards this goal, we report initial results of a new effort to develop a standardized vocabulary and ontology for insect natural history data. In particular, we describe a new database of representative insect natural history data derived from multiple sources (but focused on data from specimens in biological collections), an analysis of the abstract conceptual areas required for a comprehensive ontology of insect natural history data, and a database of use cases and competency questions to guide the development of data systems for insect natural history data. We also discuss data modeling and technology-related challenges that must be overcome to implement robust integration of insect natural history data.

scholarly journals Evolution of the C-Type Lectin-Like Receptor Genes of the DECTIN-1 Cluster in the NK Gene Complex

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Susanne Sattler ◽  
Hormas Ghadially ◽  
Erhard Hofer
Keyword(s):  
Pattern Recognition ◽  
Sequence Data ◽  
Gene Duplications ◽  
Gene Complex ◽  
Adaptive Immune ◽  
Recognition Function ◽  
Recent Developments ◽  
Evolutionary Emergence ◽  
Related Proteins ◽  
Nk Gene Complex

Pattern recognition receptors are crucial in initiating and shaping innate and adaptive immune responses and often belong to families of structurally and evolutionarily related proteins. The human C-type lectin-like receptors encoded in the DECTIN-1 cluster within the NK gene complex contain prominent receptors with pattern recognition function, such as DECTIN-1 and LOX-1. All members of this cluster share significant homology and are considered to have arisen from subsequent gene duplications. Recent developments in sequencing and the availability of comprehensive sequence data comprising many species showed that the receptors of the DECTIN-1 cluster are not only homologous to each other but also highly conserved between species. Even inCaenorhabditis elegans, genes displaying homology to the mammalian C-type lectin-like receptors have been detected. In this paper, we conduct a comprehensive phylogenetic survey and give an up-to-date overview of the currently available data on the evolutionary emergence of the DECTIN-1 cluster genes.

scholarly journals Evolution of polymer formation within the actin superfamily

2017 ◽  
Vol 28 (19) ◽  
pp. 2461-2469 ◽  
Author(s):  
Patrick R. Stoddard ◽  
Tom A. Williams ◽  
Ethan Garner ◽  
Buzz Baum
Keyword(s):  
Convergent Evolution ◽  
Atp Hydrolysis ◽  
Linear Polymers ◽  
Related Protein ◽  
Protein Families ◽  
Structure And Dynamics ◽  
Polymer Formation ◽  
Filament Structure ◽  
Related Proteins ◽  
Actin Superfamily

While many are familiar with actin as a well-conserved component of the eukaryotic cytoskeleton, it is less often appreciated that actin is a member of a large superfamily of structurally related protein families found throughout the tree of life. Actin-related proteins include chaperones, carbohydrate kinases, and other enzymes, as well as a staggeringly diverse set of proteins that use the energy from ATP hydrolysis to form dynamic, linear polymers. Despite differing widely from one another in filament structure and dynamics, these polymers play important roles in ordering cell space in bacteria, archaea, and eukaryotes. It is not known whether these polymers descended from a single ancestral polymer or arose multiple times by convergent evolution from monomeric actin-like proteins. In this work, we provide an overview of the structures, dynamics, and functions of this diverse set. Then, using a phylogenetic analysis to examine actin evolution, we show that the actin-related protein families that form polymers are more closely related to one another than they are to other nonpolymerizing members of the actin superfamily. Thus all the known actin-like polymers are likely to be the descendants of a single, ancestral, polymer-forming actin-like protein.

scholarly journals Conserved Structure and Function in the Granulysin and NK-Lysin Peptide Family

2005 ◽  
Vol 73 (10) ◽  
pp. 6332-6339 ◽  
Author(s):  
Charlotte M. A. Linde ◽  
Susanna Grundström ◽  
Erik Nordling ◽  
Essam Refai ◽  
Patrick J. Brennan ◽  
...  
Keyword(s):  
Mycobacterium Smegmatis ◽  
Three Dimensional ◽  
Antimycobacterial Activity ◽  
Structure And Function ◽  
Loop Structure ◽  
E Coli ◽  
Short Loop ◽  
Peptide Family ◽  
And Function ◽  
Related Proteins

ABSTRACT Granulysin and NK-lysin are homologous bactericidal proteins with a moderate residue identity (35%), both of which have antimycobacterial activity. Short loop peptides derived from the antimycobacterial domains of granulysin, NK-lysin, and a putative chicken NK-lysin were examined and shown to have comparable antimycobacterial but variable Escherichia coli activities. The known structure of the NK-lysin loop peptide was used to predict the structure of the equivalent peptides of granulysin and chicken NK-lysin by homology modeling. The last two adopted a secondary structure almost identical to that of NK-lysin. All three peptides form very similar three-dimensional (3-D) architectures in which the important basic residues assume the same positions in space. The basic residues in granulysin are arginine, while those in NK-lysin and chicken NK-lysin are a mixture of arginine and lysine. We altered the ratio of arginine to lysine in the granulysin fragment to examine the importance of basic residues for antimycobacterial activity. The alteration of the amino acids reduced the activity against E. coli to a larger extent than that against Mycobacterium smegmatis. In granulysin, the arginines in the loop structure are not crucial for antimycobacterial activity but are important for cytotoxicity. We suggest that the antibacterial domains of the related proteins granulysin, NK-lysin, and chicken NK-lysin have conserved their 3-D structure and their function against mycobacteria.

scholarly journals Unlocking Elementary Conversion Modes: ecmtool unveils all capabilities of metabolic networks

2020 ◽  
Author(s):  
Tom J. Clement ◽  
Erik B. Baalhuis ◽  
Bas Teusink ◽  
Frank J. Bruggeman ◽  
Robert Planqué ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Metabolic Networks ◽  
Full Range ◽  
Biotechnological Potential ◽  
Metabolic Network Reconstruction ◽  
And Function ◽  
Multicellular Organisms ◽  
Genome Scale ◽  
Threat Levels ◽  
Experimental Characterisation

AbstractThe metabolic capabilities of cells determine their biotechnological potential, fitness in ecosystems, pathogenic threat levels, and function in multicellular organisms. Their comprehensive experimental characterisation is generally not feasible, particularly for unculturable organisms. In principle, the full range of metabolic capabilities can be computed from an organism’s annotated genome using metabolic network reconstruction. However, current computational methods cannot deal with genome-scale metabolic networks. Part of the problem is that these methods aim to enumerate all metabolic pathways, while computation of all (elementally balanced) conversions between nutrients and products would suffice. Indeed, the elementary conversion modes (ECMs, defined by Urbanczik and Wagner) capture the full metabolic capabilities of a network, but the use of ECMs has not been accessible, until now. We extend and explain the theory of ECMs, implement their enumeration in ecmtool, and illustrate their applicability. This work contributes to the elucidation of the full metabolic footprint of any cell.

Sign in / Sign up

Export Citation Format

Share Document