scholarly journals Proteins Binding to the Carbohydrate HNK-1: Common Origins?

2021 ◽  
Vol 22 (15) ◽  
pp. 8116
Author(s):  
Gaston Castillo ◽  
Ralf Kleene ◽  
Melitta Schachner ◽  
Gabriele Loers ◽  
Andrew E. Torda
Keyword(s):  
Large Scale ◽  
System Development ◽  
Sequence Similarity ◽  
High Mobility ◽  
Binding Constants ◽  
Nervous System Development ◽  
Sequence Motifs ◽  
Sequence Alignments ◽  
Conserved Sequence ◽  
Bona Fide

The human natural killer (HNK-1) carbohydrate plays important roles during nervous system development, regeneration after trauma and synaptic plasticity. Four proteins have been identified as receptors for HNK-1: the laminin adhesion molecule, high-mobility group box 1 and 2 (also called amphoterin) and cadherin 2 (also called N-cadherin). Because of HNK-1′s importance, we asked whether additional receptors for HNK-1 exist and whether the four identified proteins share any similarity in their primary structures. A set of 40,000 sequences homologous to the known HNK-1 receptors was selected and used for large-scale sequence alignments and motif searches. Although there are conserved regions and highly conserved sites within each of these protein families, there was no sequence similarity or conserved sequence motifs found to be shared by all families. Since HNK-1 receptors have not been compared regarding binding constants and since it is not known whether the sulfated or non-sulfated part of HKN-1 represents the structurally crucial ligand, the receptors are more heterogeneous in primary structure than anticipated, possibly involving different receptor or ligand regions. We thus conclude that the primary protein structure may not be the sole determinant for a bona fide HNK-1 receptor, rendering receptor structure more complex than originally assumed.

scholarly journals A Comprehensive Review: Sphingolipid Metabolism and Implications of Disruption in Sphingolipid Homeostasis

2021 ◽  
Vol 22 (11) ◽  
pp. 5793
Author(s):  
Brianna M. Quinville ◽  
Natalie M. Deschenes ◽  
Alex E. Ryckman ◽  
Jagdeep S. Walia
Keyword(s):  
Nervous System ◽  
Large Scale ◽  
System Development ◽  
Building Blocks ◽  
Cell Types ◽  
Nervous System Development ◽  
Sphingolipid Metabolism ◽  
Lysosomal Storage ◽  
Bioactive Lipids ◽  
Comprehensive Review

Sphingolipids are a specialized group of lipids essential to the composition of the plasma membrane of many cell types; however, they are primarily localized within the nervous system. The amphipathic properties of sphingolipids enable their participation in a variety of intricate metabolic pathways. Sphingoid bases are the building blocks for all sphingolipid derivatives, comprising a complex class of lipids. The biosynthesis and catabolism of these lipids play an integral role in small- and large-scale body functions, including participation in membrane domains and signalling; cell proliferation, death, migration, and invasiveness; inflammation; and central nervous system development. Recently, sphingolipids have become the focus of several fields of research in the medical and biological sciences, as these bioactive lipids have been identified as potent signalling and messenger molecules. Sphingolipids are now being exploited as therapeutic targets for several pathologies. Here we present a comprehensive review of the structure and metabolism of sphingolipids and their many functional roles within the cell. In addition, we highlight the role of sphingolipids in several pathologies, including inflammatory disease, cystic fibrosis, cancer, Alzheimer’s and Parkinson’s disease, and lysosomal storage disorders.

scholarly journals Mitochondrial Association of a Plus End–Directed Microtubule Motor Expressed during Mitosis in Drosophila

1997 ◽  
Vol 136 (5) ◽  
pp. 1081-1090 ◽  
Author(s):  
Andrea J. Pereira ◽  
Brian Dalby ◽  
Russell J. Stewart ◽  
Stephen J. Doxsey ◽  
Lawrence S.B. Goldstein
Keyword(s):  
System Development ◽  
Sequence Similarity ◽  
Cell Types ◽  
Nervous System Development ◽  
In Vitro Motility Assay ◽  
Specific Expression ◽  
In Vitro Motility ◽  
Amino Terminal ◽  
Specific Expression Pattern

The kinesin superfamily is a large group of proteins (kinesin-like proteins [KLPs]) that share sequence similarity with the microtubule (MT) motor kinesin. Several members of this superfamily have been implicated in various stages of mitosis and meiosis. Here we report our studies on KLP67A of Drosophila. DNA sequence analysis of KLP67A predicts an MT motor protein with an amino-terminal motor domain. To prove this directly, KLP67A expressed in Escherichia coli was shown in an in vitro motility assay to move MTs in the plus direction. We also report expression analyses at both the mRNA and protein level, which implicate KLP67A in the localization of mitochondria in undifferentiated cell types. In situ hybridization studies of the KLP67A mRNA during embryogenesis and larval central nervous system development indicate a proliferation-specific expression pattern. Furthermore, when affinity-purified anti-KLP67A antisera are used to stain blastoderm embryos, mitochondria in the region of the spindle asters are labeled. These data suggest that KLP67A is a mitotic motor of Drosophila that may have the unique role of positioning mitochondria near the spindle.

scholarly journals Point Mutations in Yeast CBF5 Can Abolish In Vivo Pseudouridylation of rRNA

1999 ◽  
Vol 19 (11) ◽  
pp. 7461-7472 ◽  
Author(s):  
Yeganeh Zebarjadian ◽  
Tom King ◽  
Maurille J. Fournier ◽  
Louise Clarke ◽  
John Carbon
Keyword(s):  
Catalytic Domain ◽  
Sequence Similarity ◽  
Point Mutations ◽  
Rrna Synthesis ◽  
Temperature Sensitive ◽  
In Vitro Mutagenesis ◽  
Sequence Motifs ◽  
Conserved Sequence

ABSTRACT In budding yeast (Saccharomyces cerevisiae), the majority of box H/ACA small nucleolar RNPs (snoRNPs) have been shown to direct site-specific pseudouridylation of rRNA. Among the known protein components of H/ACA snoRNPs, the essential nucleolar protein Cbf5p is the most likely pseudouridine (Ψ) synthase. Cbf5p has considerable sequence similarity to Escherichia coli TruBp, a known Ψ synthase, and shares the “KP” and “XLD” conserved sequence motifs found in the catalytic domains of three distinct families of known and putative Ψ synthases. To gain additional evidence on the role of Cbf5p in rRNA biosynthesis, we have used in vitro mutagenesis techniques to introduce various alanine substitutions into the putative Ψ synthase domain of Cbf5p. Yeast strains expressing these mutatedcbf5 genes in a cbf5Δ null background are viable at 25°C but display pronounced cold- and heat-sensitive growth phenotypes. Most of the mutants contain reduced levels of Ψ in rRNA at extreme temperatures. Substitution of alanine for an aspartic acid residue in the conserved XLD motif of Cbf5p (mutantcbf5D95A) abolishes in vivo pseudouridylation of rRNA. Some of the mutants are temperature sensitive both for growth and for formation of Ψ in the rRNA. In most cases, the impaired growth phenotypes are not relieved by transcription of the rRNA from a polymerase II-driven promoter, indicating the absence of polymerase I-related transcriptional defects. There is little or no abnormal accumulation of pre-rRNAs in these mutants, although preferential inhibition of 18S rRNA synthesis is seen in mutantcbf5D95A, which lacks Ψ in rRNA. A subset of mutations in the Ψ synthase domain impairs association of the altered Cbf5p proteins with selected box H/ACA snoRNAs, suggesting that the functional catalytic domain is essential for that interaction. Our results provide additional evidence that Cbf5p is the Ψ synthase component of box H/ACA snoRNPs and suggest that the pseudouridylation of rRNA, although not absolutely required for cell survival, is essential for the formation of fully functional ribosomes.

scholarly journals High-resolution structure of NodZ fucosyltransferase involved in the biosynthesis of the nodulation factor.

2007 ◽  
Vol 54 (3) ◽  
pp. 537-549 ◽  
Author(s):  
Krzysztof Brzezinski ◽  
Tomasz Stepkowski ◽  
Santosh Panjikar ◽  
Grzegorz Bujacz ◽  
Mariusz Jaskolski
Keyword(s):  
Catalytic Mechanism ◽  
Broad Class ◽  
Sequence Motifs ◽  
Sequence Alignments ◽  
Crystal Forms ◽  
Conserved Sequence ◽  
Terminal Domain ◽  
Phosphate Ions ◽  
High Resolution Structure ◽  
Nodulation Factor

The fucosyltransferase NodZ is involved in the biosynthesis of the nodulation factor in nitrogen-fixing symbiotic bacteria. It catalyzes alpha1,6 transfer of l-fucose from GDP-fucose to the reducing residue of the synthesized Nod oligosaccharide. We present the structure of the NodZ protein from Bradyrhizobium expressed in Escherichia coli and crystallized in the presence of phosphate ions in two crystal forms. The enzyme is arranged into two domains of nearly equal size. Although NodZ falls in one broad class (GT-B) with other two-domain glycosyltransferases, the topology of its domains deviates from the canonical Rossmann fold, with particularly high distortions in the N-terminal domain. Mutational data combined with structural and sequence alignments indicate residues of potential importance in GDP-fucose binding or in the catalytic mechanism. They are all clustered in three conserved sequence motifs located in the C-terminal domain.

scholarly journals Dynamic Expression of Long Non-Coding RNAs Throughout Parasite Sexual and Neural Maturation in Schistosoma Japonicum

2020 ◽  
Vol 6 (2) ◽  
pp. 15 ◽  
Author(s):  
Lucas Maciel ◽  
David Morales-Vicente ◽  
Sergio Verjovski-Almeida
Keyword(s):  
Schistosoma Japonicum ◽  
Sexual Maturation ◽  
System Development ◽  
Sequence Similarity ◽  
Nervous System Development ◽  
Rna Seq ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Synteny Conservation ◽  
Non Coding Rnas

Schistosoma japonicum is a flatworm that causes schistosomiasis, a neglected tropical disease. S. japonicum RNA-Seq analyses has been previously reported in the literature on females and males obtained during sexual maturation from 14 to 28 days post-infection in mouse, resulting in the identification of protein-coding genes and pathways, whose expression levels were related to sexual development. However, this work did not include an analysis of long non-coding RNAs (lncRNAs). Here, we applied a pipeline to identify and annotate lncRNAs in 66 S. japonicum RNA-Seq publicly available libraries, from different life-cycle stages. We also performed co-expression analyses to find stage-specific lncRNAs possibly related to sexual maturation. We identified 12,291 S. japonicum expressed lncRNAs. Sequence similarity search and synteny conservation indicated that some 14% of S. japonicum intergenic lncRNAs have synteny conservation with S. mansoni intergenic lncRNAs. Co-expression analyses showed that lncRNAs and protein-coding genes in S. japonicum males and females have a dynamic co-expression throughout sexual maturation, showing differential expression between the sexes; the protein-coding genes were related to the nervous system development, lipid and drug metabolism, and overall parasite survival. Co-expression pattern suggests that lncRNAs possibly regulate these processes or are regulated by the same activation program as that of protein-coding genes.

scholarly journals Mapping the Intramolecular Communications among Different Glutamate Dehydrogenase States Using Molecular Dynamics

Biomolecules ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 798
Author(s):  
Shaherin Basith ◽  
Balachandran Manavalan ◽  
Tae Hwan Shin ◽  
Gwang Lee
Keyword(s):  
Network Analysis ◽  
Glutamate Dehydrogenase ◽  
Conformational Changes ◽  
Large Scale ◽  
Structural Information ◽  
System Development ◽  
Enzyme Regulation ◽  
Nervous System Development ◽  
Dynamic Simulations ◽  
Carbon And Nitrogen

Glutamate dehydrogenase (GDH) is a ubiquitous enzyme that catalyzes the reversible oxidative deamination of glutamate to α-ketoglutarate. It acts as an important branch-point enzyme between carbon and nitrogen metabolisms. Due to the multifaceted roles of GDH in cancer, hyperinsulinism/hyperammonemia, and central nervous system development and pathologies, tight control of its activity is necessitated. To date, several GDH structures have been solved in its closed form; however, intrinsic structural information in its open and apo forms are still deficient. Moreover, the allosteric communications and conformational changes taking place in the three different GDH states are not well studied. To mitigate these drawbacks, we applied unbiased molecular dynamic simulations (MD) and network analysis to three different GDH states i.e., apo, active, and inactive forms, for investigating their modulatory mechanisms. In this paper, based on MD and network analysis, crucial residues important for signal transduction, conformational changes, and maps of information flow among the different GDH states were elucidated. Moreover, with the recent findings of allosteric modulators, an allosteric wiring illustration of GDH intramolecular signal transductions would be of paramount importance to obtain the process of this enzyme regulation. The structural insights gained from this study will pave way for large-scale screening of GDH regulators and could support researchers in the design and development of new and potent GDH ligands.

scholarly journals Database Mining for Novel Bacterial β-Etherases, Glutathione-Dependent Lignin-Degrading Enzymes

2019 ◽  
Vol 86 (2) ◽  
Author(s):  
Hauke Voß ◽  
Carina Amata Heck ◽  
Marcus Schallmey ◽  
Anett Schallmey
Keyword(s):  
Biochemical Characterization ◽  
Phylogenetic Analyses ◽  
Sequence Motifs ◽  
Database Mining ◽  
Sequence Alignments ◽  
Renewable Source ◽  
Aromatic Polymer ◽  
Conserved Sequence ◽  
Peptide Pattern ◽  
Lignin Depolymerization

ABSTRACT Lignin is the most abundant aromatic polymer in nature and a promising renewable source for the provision of aromatic platform chemicals and biofuels. β-Etherases are enzymes with a promising potential for application in lignin depolymerization due to their selectivity in the cleavage of β-O-4 aryl ether bonds. However, only a very limited number of these enzymes have been described and characterized so far. Using peptide pattern recognition (PPR) as well as phylogenetic analyses, 96 putatively novel β-etherases have been identified, some even originating from bacteria outside the order Sphingomonadales. A set of 13 diverse enzymes was selected for biochemical characterization, and β-etherase activity was confirmed for all of them. Some enzymes displayed up to 3-fold higher activity than previously known β-etherases. Moreover, conserved sequence motifs specific for either LigE- or LigF-type enzymes were deduced from multiple-sequence alignments and the PPR-derived peptides. In combination with structural information available for the β-etherases LigE and LigF, insight into the potential structural and/or functional role of conserved residues within these sequence motifs is provided. Phylogenetic analyses further suggest the presence of additional bacterial enzymes with potential β-etherase activity outside the classical LigE- and LigF-type enzymes as well as the recently described heterodimeric β-etherases. IMPORTANCE The use of biomass as a renewable source and replacement for crude oil for the provision of chemicals and fuels is of major importance for current and future societies. Lignin, the most abundant aromatic polymer in nature, holds promise as a renewable starting material for the generation of required aromatic structures. However, a controlled and selective lignin depolymerization to yield desired aromatic structures is a very challenging task. In this regard, bacterial β-etherases are especially interesting, as they are able to cleave the most abundant bond type in lignin with high selectivity. With this study, we significantly expanded the toolbox of available β-etherases for application in lignin depolymerization and discovered more active as well as diverse enzymes than previously known. Moreover, the identification of further β-etherases by sequence database mining in the future will be facilitated considerably through our deduced etherase-specific sequence motifs.

scholarly journals Characterization of an Extremely Thermostable Restriction Enzyme, PspGI, from a PyrococcusStrain and Cloning of the PspGI Restriction-Modification System in Escherichia coli

1998 ◽  
Vol 64 (10) ◽  
pp. 3669-3673 ◽  
Author(s):  
Richard Morgan ◽  
Jian-ping Xiao ◽  
Shuang-yong Xu
Keyword(s):  
Escherichia Coli ◽  
Sequence Similarity ◽  
Expression System ◽  
Sequence Motifs ◽  
Recognition Sequence ◽  
Modification System ◽  
Conserved Sequence ◽  
Restriction Modification System ◽  
Diagnostic Applications ◽  
Restriction Modification

ABSTRACT An extremely thermostable restriction endonuclease,PspGI, was purified from Pyrococcus sp. strain GI-H. PspGI is an isoschizomer of EcoRII and cleaves DNA before the first C in the sequence 5′ ^CCWGG 3′ (W is A or T). PspGI digestion can be carried out at 65 to 85°C. To express PspGI at high levels, the PspGI restriction-modification genes (pspGIR andpspGIM) were cloned in Escherichia coli. M.PspGI contains the conserved sequence motifs of α-aminomethyltransferases; therefore, it must be an N4-cytosine methylase. M.PspGI shows 53% similarity to (44% identity with) its isoschizomer, M.MvaI fromMicrococcus variabilis. In a segment of 87 amino acid residues, PspGI shows significant sequence similarity toEcoRII and to regions of SsoII andStyD4I which have a closely related recognition sequence (5′ ^CCNGG 3′). PspGI was expressed in E. coli via a T7 expression system. Recombinant PspGI was purified to near homogeneity and had a half-life of 2 h at 95°C. PspGI remained active following 30 cycles of thermocycling; thus, it can be used in DNA-based diagnostic applications.

scholarly journals The genetic factors of bilaterian evolution

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Peter Heger ◽  
Wen Zheng ◽  
Anna Rottmann ◽  
Kristen A Panfilio ◽  
Thomas Wiehe
Keyword(s):  
Evolutionary Biology ◽  
Large Scale ◽  
System Development ◽  
Full Range ◽  
Nervous System Development ◽  
Cambrian Explosion ◽  
Current View ◽  
Mesoderm Development ◽  
System A ◽  
Genetic Mechanisms

The Cambrian explosion was a unique animal radiation ~540 million years ago that produced the full range of body plans across bilaterians. The genetic mechanisms underlying these events are unknown, leaving a fundamental question in evolutionary biology unanswered. Using large-scale comparative genomics and advanced orthology evaluation techniques, we identified 157 bilaterian-specific genes. They include the entire Nodal pathway, a key regulator of mesoderm development and left-right axis specification; components for nervous system development, including a suite of G-protein-coupled receptors that control physiology and behaviour, the Robo-Slit midline repulsion system, and the neurotrophin signalling system; a high number of zinc finger transcription factors; and novel factors that previously escaped attention. Contradicting the current view, our study reveals that genes with bilaterian origin are robustly associated with key features in extant bilaterians, suggesting a causal relationship.

scholarly journals HH-suite3 for fast remote homology detection and deep protein annotation

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Martin Steinegger ◽  
Markus Meier ◽  
Milot Mirdita ◽  
Harald Vöhringer ◽  
Stephan J. Haunsberger ◽  
...  
Keyword(s):  
Open Source ◽  
Large Scale ◽  
Message Passing Interface ◽  
Viterbi Algorithm ◽  
Sequence Similarity ◽  
Pairwise Alignment ◽  
Homology Detection ◽  
Sequence Alignments ◽  
Homologous Proteins ◽  
Multiple Sequence

Abstract Background HH-suite is a widely used open source software suite for sensitive sequence similarity searches and protein fold recognition. It is based on pairwise alignment of profile Hidden Markov models (HMMs), which represent multiple sequence alignments of homologous proteins. Results We developed a single-instruction multiple-data (SIMD) vectorized implementation of the Viterbi algorithm for profile HMM alignment and introduced various other speed-ups. These accelerated the search methods HHsearch by a factor 4 and HHblits by a factor 2 over the previous version 2.0.16. HHblits3 is ∼10× faster than PSI-BLAST and ∼20× faster than HMMER3. Jobs to perform HHsearch and HHblits searches with many query profile HMMs can be parallelized over cores and over cluster servers using OpenMP and message passing interface (MPI). The free, open-source, GPLv3-licensed software is available at https://github.com/soedinglab/hh-suite. Conclusion The added functionalities and increased speed of HHsearch and HHblits should facilitate their use in large-scale protein structure and function prediction, e.g. in metagenomics and genomics projects.

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