scholarly journals Cloning and sequencing of four new mammalian monocarboxylate transporter (MCT) homologues confirms the existence of a transporter family with an ancient past

1998 ◽  
Vol 329 (2) ◽  
pp. 321-328 ◽  
Author(s):  
T. Nigel PRICE ◽  
N. Vicky JACKSON ◽  
P. Andrew HALESTRAP
Keyword(s):  
Monocarboxylate Transporter ◽  
Cdna Libraries ◽  
Sequence Motifs ◽  
Intracellular Loop ◽  
Cloning And Sequencing ◽  
Sequence Alignments ◽  
Yeast Saccharomyces Cerevisiae ◽  
Multiple Sequence ◽  
Conserved Sequence ◽  
Transporter Family

Measurement of monocarboxylate transport kinetics in a range of cell types has provided strong circumstantial evidence for a family of monocarboxylate transporters (MCTs). Two mammalian MCT isoforms (MCT1 and MCT2) and a chicken isoform (REMP or MCT3) have already been cloned, sequenced and expressed, and another MCT-like sequence (XPCT) has been identified. Here we report the identification of new human MCT homologues in the database of expression sequence tags and the cloning and sequencing of four new full-length MCT-like sequences from human cDNA libraries, which we have denoted MCT3, MCT4, MCT5 and MCT6. Northern blotting revealed a unique tissue distribution for the expression of mRNA for each of the seven putative MCT isoforms (MCT1-MCT6 and XPCT). All sequences were predicted to have 12 transmembrane (TM) helical domains with a large intracellular loop between TM6 and TM7. Multiple sequence alignments showed identities ranging from 20% to 55%, with the greatest conservation in the predicted TM regions and more variation in the C-terminal than the N-terminal region. Searching of additional sequence databases identified candidate MCT homologues from the yeast Saccharomyces cerevisiae, the nematode worm Caenorhabditis elegans and the archaebacterium Sulfolobus solfataricus. Together these sequences constitute a new family of transporters with some strongly conserved sequence motifs, the possible functions of which are discussed.

Evolutionary History of Plant Lipolytic Enzymes

2018 ◽  
pp. 155-178
Keyword(s):  
Higher Plants ◽  
Evolutionary Relationship ◽  
Biological Evolution ◽  
Sequence Motifs ◽  
Multiple Sequence ◽  
Lipolytic Enzymes ◽  
Conserved Sequence ◽  
Potential Applications ◽  
History Of ◽  
Living Organisms

The discovery of enzymes with lipolytic activities in all kingdoms of life from prokaryote to eukaryote species raises the possibility of the presence of an evolutionary relationship history of these proteins among many species of various living organisms. The chapter suggests a strategy based on the phylogenetic distribution and homology conservation in plant lipolytic enzymes for possible depiction of their biological evolution. Extensive databases and online resources for lipidomics and related areas are useful tools to analyze the different lipolytic enzymes in the three major super kingdoms of life, including higher plants kingdom and confined organisms such as algae that have recently gained much interest due to their promising potential applications in lipids hydrolysis and biosynthesis. Multiple sequence alignments of the identified lipolytic enzymes from databases could serve to the identification of globally conserved residues as well as conserved sequence motifs. Estimation of evolutionary distance between the various identified lipolytic enzymes could also be carried out to better understand the pattern of evolution.

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 Evolutionary Relationships and Sequence-Structure Determinants in Human SARS Coronavirus-2 Spike Proteins for Host Receptor Recognition

2020 ◽  
Author(s):  
Lalitha Guruprasad
Keyword(s):  
Phylogenetic Trees ◽  
Disulfide Bridge ◽  
Sequence Motifs ◽  
Structural Determinants ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Angiotensin Converting Enzyme 2 ◽  
Multiple Sequence Alignments ◽  
Loop 2 ◽  
Spike Proteins

<div>Coronavirus disease 2019 (COVID-19) is a pandemic infectious disease caused by novel Severe Acute Respiratory Syndrome coronavirus-2 (SARS CoV-2). The SARS CoV-2 is transmitted more rapidly and readily than SARS CoV. Both, SARS CoV and SARS CoV-2 via their glycosylated spike proteins recognize the human angiotensin converting enzyme-2 (ACE-2) receptor. We generated multiple sequence alignments and phylogenetic trees for representative spike proteins of CoV and CoV-2 from various host sources in order to analyze the specificity in SARS CoV-2 spike proteins required for causing infection in humans. Our results show that two sequence motifs in the N-terminal domain; "MESEFR" and "SYLTPG" are specific to human SARS CoV-2 and pangolin SARS CoV. In the receptor binding domain (RBD), three sequence loops; VGGNY (loop 1), YQAGSTPC (loop 2), EGFNCY (loop 3) and a tethered disulfide bridge Cys480-Cys488 connecting loops 2 and 3 are structural determinants for the recognition of human ACE-2 receptor. The complete genome analysis of representative SARS CoVs from bat, civet, pangolin, human host sources and human SARS CoV-2 identified the bat genome (GenBank code: MN996532.1) and the pangolin SARS CoV genomes as closest to the recent novel human SARS CoV-2 genomes. The bat CoV genomes (GenBank codes: MG772933 and MG772934) are evolutionary intermediates in the mutagenesis progression towards becoming human SARS CoV-2. </div>

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 Survey of the use of genetic algorithm for multiple sequence alignment

2016 ◽  
Vol 5 (2) ◽  
pp. 28
Author(s):  
Mohamed Tahar Ben Othman
Keyword(s):  
Genetic Algorithms ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Genomic Analysis ◽  
Evolutionary Divergence ◽  
Sequence Motifs ◽  
Property A ◽  
Multiple Sequence ◽  
Complete Class ◽  
Conserved Sequence

Multiple Sequence Alignment (MSA) is used in genomic analysis, such as the identification of conserved sequence motifs, the estimation of evolutionary divergence between sequences, and the genes’ historical relationships inference. Several researches were conducted to determine the level of similarity of a set of sequences. Due to the problem of the NP-complete class property, a number of researches use genetic algorithms (GA) to find a solution to the multiple sequence alignment. However, the nature of genetic algorithms makes the complexity extremely high due to the redundancy provided by the different operators. The aim of this paper is to study some proposed GA solutions provided for MSA and to compare them using some criteria which we believe any solution should comply with in matters of representativeness, closeness and original sequence invariance.

scholarly journals Plastics degradation by hydrolytic enzymes: the Plastics-Active Enzymes Database - PAZy

2021 ◽  
Author(s):  
Patrick Buchholz ◽  
Hongli Zhang ◽  
Pablo Perez-Garcia ◽  
Lena-Luisa Nover ◽  
Jennifer Chow ◽  
...  
Keyword(s):  
Markov Models ◽  
Hydrolytic Enzymes ◽  
Ecological Niches ◽  
Structural Description ◽  
Sequence Motifs ◽  
Sequence Alignments ◽  
Activity Data ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Open Access Database

Petroleum based plastics are durable and accumulate in all ecological niches. Knowledge on enzymatic degradation is sparse. Today, less than 50 verified plastics-active enzymes are known. First examples of enzymes acting on the polymers polyethylene terephthalate (PET) and polyurethane (PUR) have been reported together with a detailed biochemical and structural description. Further, very few polyamide (PA) oligomer active enzymes are known. In this paper, the current known enzymes acting on the synthetic polymers PET and PUR are briefly summarized, their published activity data were collected and integrated into a comprehensive open access database. The Plastics-Active Enzymes Database (PAZy) represents an inventory of known and experimentally verified plastics-active enzymes. Almost 3000 homologues of PET-active enzymes were identified by profile hidden Markov models. Over 2000 homologues of PUR-active enzymes were identified by BLAST. Based on multiple sequence alignments, conservation analysis identified the most conserved amino acids, and sequence motifs for PET- and PUR-active enzymes were derived.

scholarly journals Evolutionary Relationships and Sequence-Structure Determinants in Human SARS Coronavirus-2 Spike Proteins for Host Receptor Recognition

2020 ◽  
Author(s):  
Lalitha Guruprasad
Keyword(s):  
Phylogenetic Trees ◽  
Disulfide Bridge ◽  
Sequence Motifs ◽  
Structural Determinants ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Angiotensin Converting Enzyme 2 ◽  
Multiple Sequence Alignments ◽  
Loop 2 ◽  
Spike Proteins

Coronavirus disease 2019 (COVID-19) is a pandemic infectious disease caused by novel Severe Acute Respiratory Syndrome coronavirus-2 (SARS CoV-2). The SARS CoV-2 is transmitted more rapidly and readily than SARS CoV. Both, SARS CoV and SARS CoV-2 via their glycosylated spike proteins recognize the human angiotensin converting enzyme-2 (ACE-2) receptor. We generated multiple sequence alignments and phylogenetic trees for representative spike proteins of CoV and CoV-2 from various host sources in order to analyze the specificity in SARS CoV-2 spike proteins required for causing infection in humans. Our results show that two sequence motifs in the N-terminal domain; "MESEFR" and "SYLTPG" are specific to human SARS CoV-2 and pangolin SARS CoV. In the receptor binding domain (RBD), three sequence loops; VGGNY (loop 1), YQAGSTPC (loop 2), EGFNCY (loop 3) and a tethered disulfide bridge Cys480-Cys488 connecting loops 2 and 3 are structural determinants for the recognition of human ACE-2 receptor. The complete genome analysis of representative SARS CoVs from bat, civet, pangolin, human host sources and human SARS CoV-2 identified the bat genome (GenBank code: MN996532.1) and the pangolin SARS CoV genomes as closest to the recent novel human SARS CoV-2 genomes. The bat CoV genomes (GenBank codes: MG772933 and MG772934) are evolutionary intermediates in the mutagenesis progression towards becoming human SARS CoV-2.

scholarly journals Evolutionary Relationships and Sequence-Structure Determinants in Human SARS Coronavirus-2 Spike Proteins for Host Receptor Recognition

2020 ◽  
Author(s):  
Lalitha Guruprasad
Keyword(s):  
Phylogenetic Trees ◽  
Disulfide Bridge ◽  
Sequence Motifs ◽  
Structural Determinants ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Angiotensin Converting Enzyme 2 ◽  
Multiple Sequence Alignments ◽  
Complete Genome Analysis ◽  
Spike Proteins

<div>Coronavirus disease 2019 (COVID-19) is a pandemic infectious disease caused by novel Severe Acute Respiratory Syndrome coronavirus-2 (SARS CoV-2). The SARS CoV-2 is transmitted more rapidly and readily than SARS CoV. Both, SARS CoV and SARS CoV-2 via their glycosylated spike proteins recognize the human angiotensin converting enzyme-2 (ACE-2) receptor. We generated multiple sequence alignments and phylogenetic trees for representative spike proteins of CoV and CoV-2 from various host sources in order to analyze the specificity in SARS CoV-2 spike proteins required for causing infection in humans. Our results show that two sequence motifs in the N-terminal domain; "MESEFR" and "SYLTPG" are specific to human SARS CoV-2. In the receptor binding domain (RBD), two sequence motifs; "VGGNY" and "EIYQAGSTPCNGV" and a disulfide bridge connecting 480C and 488C in the extended loop are structural determinants for the recognition of human ACE-2 receptor. The complete genome analysis of representative SARS CoVs from bat, civet, human host sources and human SARS CoV-2 identified the bat genome (GenBank code: MN996532.1) as closest to the recent novel human SARS CoV-2 genomes. The bat CoV genomes (GenBank codes: MG772933 and MG772934) are evolutionary intermediates in the mutagenesis progression towards becoming human SARS CoV-2. <br></div>

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.

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