scholarly journals A Comprehensive Phylogenetic and Bioinformatics Survey of Lectins in the Fungal Kingdom

2021 ◽  
Vol 7 (6) ◽  
pp. 453
Author(s):  
Annie Lebreton ◽  
François Bonnardel ◽  
Yu-Cheng Dai ◽  
Anne Imberty ◽  
Francis M. Martin ◽  
...  
Keyword(s):  
Evolutionary Relationship ◽  
Large Family ◽  
Gene Families ◽  
Carbohydrate Binding ◽  
Sequence Motifs ◽  
Fungal Lectin ◽  
Quaternary Structures ◽  
High Degree ◽  
Carbohydrate Ligand ◽  
Fungal Kingdom

Fungal lectins are a large family of carbohydrate-binding proteins with no enzymatic activity. They play fundamental biological roles in the interactions of fungi with their environment and are found in many different species across the fungal kingdom. In particular, their contribution to defense against feeders has been emphasized, and when secreted, lectins may be involved in the recognition of bacteria, fungal competitors and specific host plants. Carbohydrate specificities and quaternary structures vary widely, but evidence for an evolutionary relationship within the different classes of fungal lectins is supported by a high degree of amino acid sequence identity. The UniLectin3D database contains 194 fungal lectin 3D structures, of which 129 are characterized with a carbohydrate ligand. Using the UniLectin3D lectin classification system, 109 lectin sequence motifs were defined to screen 1223 species deposited in the genomic portal MycoCosm of the Joint Genome Institute. The resulting 33,485 putative lectin sequences are organized in MycoLec, a publicly available and searchable database. These results shed light on the evolution of the lectin gene families in fungi.

scholarly journals A Comprehensive Phylogenetic and Bioinformatics Survey of Lectins in the Fungal kingdom

2021 ◽  
Author(s):  
Annie Lebreton ◽  
Francois Bonnardel ◽  
Yu-Cheng Dai ◽  
Anne Imberty ◽  
Francis M Martin ◽  
...  
Keyword(s):  
Amino Acid ◽  
Evolutionary Relationship ◽  
Large Family ◽  
Gene Families ◽  
Carbohydrate Ligands ◽  
Fungal Genomes ◽  
Quaternary Structures ◽  
High Degree ◽  
Carbohydrate Ligand ◽  
Fungal Kingdom

Fungal lectins are a large family of glycan-binding proteins, with no enzymatic activity. They play fundamental biological roles in the interactions of fungi with their environment and are found in many different species throughout the fungal kingdom. In particular, their contribution to defence against feeders has been emphasized and extracellular lectins may be involved in the recognition of bacteria, fungal competitors and specific host plants. Their carbohydrate specificities and quaternary structures vary widely, but evidence for an evolutionary relationship within the different classes of lectins is provided by the high degree of amino acid sequence identity shared by the different fungal lectins. The UniLectin3D database contains 194 3D structures of fungal lectins, of which 129 are characterized with their carbohydrate ligand. UniLectin3D lectin classes from all origins were used to construct 107 lectin motifs in 26 folding configurations and to screen 1,223 species deposited in the genomic portal MycoCosm of the Joint Genome Institute. The resulting 33 485 protein sequences of putative lectins are organized in MycoLec, a publicly available and searchable database. The charac-terization of the lectin candidates in fungal genomes is based on systematic statistics regarding po-tential carbohydrate ligands, protein lengths, signal peptides, relative motif positions and amino acid compositions of fungal lectins. These results shed light on the evolution of the lectin gene families.

scholarly journals Comprehensive Analysis of the Histone Deacetylase Gene Family in Chinese Cabbage (Brassica rapa): From Evolution and Expression Pattern to Functional Analysis of BraHDA3

Agriculture ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 244
Author(s):  
Seung Hee Eom ◽  
Tae Kyung Hyun
Keyword(s):  
Functional Analysis ◽  
Brassica Rapa ◽  
Chinese Cabbage ◽  
Stress Responses ◽  
Histone Deacetylases ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Gene Families ◽  
Physiological Processes ◽  
Lysine Residues

Histone deacetylases (HDACs) are known as erasers that remove acetyl groups from lysine residues in histones. Although plant HDACs play essential roles in physiological processes, including various stress responses, our knowledge concerning HDAC gene families and their evolutionary relationship remains limited. In Brassica rapa genome, we identified 20 HDAC genes, which are divided into three major groups: RPD3/HDA1, HD2, and SIR2 families. In addition, seven pairs of segmental duplicated paralogs and one pair of tandem duplicated paralogs were identified in the B. rapa HDAC (BraHDAC) family, indicating that segmental duplication is predominant for the expansion of the BraHDAC genes. The expression patterns of paralogous gene pairs suggest a divergence in the function of BraHDACs under various stress conditions. Furthermore, we suggested that BraHDA3 (homologous of Arabidopsis HDA14) encodes the functional HDAC enzyme, which can be inhibited by Class I/II HDAC inhibitor SAHA. As a first step toward understanding the epigenetic responses to environmental stresses in Chinese cabbage, our results provide a solid foundation for functional analysis of the BraHDAC family.

scholarly journals Olfactory expression of trace amine-associated receptors requires cooperative cis-acting enhancers

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ami Shah ◽  
Madison Ratkowski ◽  
Alessandro Rosa ◽  
Paul Feinstein ◽  
Thomas Bozza
Keyword(s):  
Gene Expression ◽  
Large Family ◽  
Sequence Motifs ◽  
Specific Expression ◽  
Cis Acting ◽  
Conserved Sequence ◽  
Trace Amine ◽  
Sequence Elements ◽  
Cell Type Specific Expression ◽  
Cell Type Specific

AbstractOlfactory sensory neurons express a large family of odorant receptors (ORs) and a small family of trace amine-associated receptors (TAARs). While both families are subject to so-called singular expression (expression of one allele of one gene), the mechanisms underlying TAAR gene choice remain obscure. Here, we report the identification of two conserved sequence elements in the mouse TAAR cluster (T-elements) that are required for TAAR gene expression. We observed that cell-type-specific expression of a TAAR-derived transgene required either T-element. Moreover, deleting either element reduced or abolished expression of a subset of TAAR genes, while deleting both elements abolished olfactory expression of all TAARs in cis with the mutation. The T-elements exhibit several features of known OR enhancers but also contain highly conserved, unique sequence motifs. Our data demonstrate that TAAR gene expression requires two cooperative cis-acting enhancers and suggest that ORs and TAARs share similar mechanisms of singular expression.

Audiological Features and Mitochondrial DNA Sequence in a Large Family Carrying Mitochondrial A1555G Mutation without Use of Aminoglycoside

2005 ◽  
Vol 114 (2) ◽  
pp. 153-160 ◽  
Author(s):  
Tatsuo Matsunaga ◽  
Hiroshi Kumanomido ◽  
Yu-ichi Goto ◽  
Masae Shiroma ◽  
Shin-ichi Usami
Keyword(s):  
Hearing Loss ◽  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Large Family ◽  
Outer Hair Cells ◽  
Japanese Family ◽  
A1555g Mutation ◽  
Genetic Mechanisms ◽  
High Degree ◽  
Sibling Group

To elucidate the pathophysiological and genetic mechanisms of hearing loss associated with the homoplasmic mitochondrial A1555G mutation in the absence of aminoglycoside exposure, we conducted audiological and genetic analyses on 67 maternally related members of a large Japanese family carrying this mutation. A consistent pattern was evident in the audiograms, with features of sensory presbycusis, cochlear origin at all levels of hearing loss, and a high degree of vulnerability of outer hair cells. That the degree of hearing loss was similar in affected subjects within the same sibling group but differed between sibling groups suggests the involvement of nuclear modifier genes. Total mitochondrial DNA sequences were completely identical among subjects with various levels of hearing loss, and lacked additional pathogenic mutations. For the diagnosis of sensorineural hearing loss, the mitochondrial A1555G mutation should be considered when these features are present even in the absence of aminoglycoside exposure.

scholarly journals Polymorphisms and gene expression in the almond IGT family are not correlated to variability in growth habit in major commercial almond cultivars

2021 ◽  
Author(s):  
Álvaro Montesinos ◽  
Chris Dardick ◽  
María José Rubio-Cabetas ◽  
Jérôme Grimplet
Keyword(s):  
Gene Expression ◽  
Critical Role ◽  
Gene Families ◽  
Fruit Trees ◽  
Hormonal Responses ◽  
Breeding Programs ◽  
Branch Angle ◽  
Conserved Domain ◽  
Family Gene ◽  
High Degree

Almond breeding programs aimed at selecting cultivars adapted to intensive orchards have recently focused on the optimization of tree architecture. This multifactorial trait is defined by numerous components controlled by processes such as hormonal responses, gravitropism and light perception. Gravitropism sensing is crucial to control the branch angle and therefore, the tree habit. A gene family, denominated IGT family after a share conserved domain, has been described as involved in the regulation of branch angle in several species, including rice and Arabidopsis, and even in fruit trees like peach. Here we identified six members of this family in almond: LAZY1 , LAZY2 , TAC1 , DRO1 , DRO2 , IGT-like . After analyzing their protein sequences in forty-one almond cultivars and wild species, little variability was found, pointing a high degree of conservation in this family. Gene expression was analyzed in fourteen cultivars of agronomical interest comprising diverse tree habit phenotypes. Only LAZY1 , LAZY2 and TAC1 were expressed in almond shoot tips during the growing season. No relation was established between the expression profile of these genes and the tree habit. However, some insight has been gained in how LAZY1 and LAZY2 are regulated, identifying the IPA1 almond homologues and other transcription factors involved in hormonal responses as regulators of their expression. Besides, we have found various polymorphisms that could not be discarded as involved in a potential polygenic origin of regulation of architectural phenotypes. Therefore, we have established that unlike many species, IGT family genes do not play a critical role in the control of tree habit in currently commercialized almond cultivars, with other gene families contributing to the variability of these traits.

Interferon-induced guanylate-binding proteins lack an N(T)KXD consensus motif and bind GMP in addition to GDP and GTP

1991 ◽  
Vol 11 (9) ◽  
pp. 4717-4725
Author(s):  
Y S Cheng ◽  
C E Patterson ◽  
P Staeheli
Keyword(s):  
Binding Proteins ◽  
Nucleotide Binding ◽  
Binding Activity ◽  
Guanine Nucleotides ◽  
Sequence Motifs ◽  
Consensus Motif ◽  
Gtp Binding ◽  
Genes Encoding ◽  
Nucleotide Binding Proteins ◽  
High Degree

The primary structures of interferon (IFN)-induced guanylate-binding proteins (GBPs) were deduced from cloned human and murine cDNAs. These proteins contained only two of the three sequence motifs typically found in GTP/GDP-binding proteins. The N(T)KXD motif, which is believed to confer guanine specificity in other nucleotide-binding proteins, was absent. Nevertheless, the IFN-induced GBPs exhibited a high degree of selectivity for binding to agarose-immobilized guanine nucleotides. An interesting feature of IFN-induced GBPs is that they strongly bound to GMP agarose in addition to GDP and GTP agaroses but failed to bind to ATP agarose and all other nucleotide agaroses tested. Both GTP and GMP, but not ATP, competed for binding of murine GBP-1 to agarose-immobilized GMP. The IFN-induced GBPs thus define a distinct novel family of proteins with GTP-binding activity. We further demonstrate that human and murine cells contain at least two genes encoding IFN-induced GBPs. The cloned murine cDNA codes for GBP-1, an IFN-induced protein previously shown to be absent from mice of Gbp-1b genotype.

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 A mutation of the common receptor subunit for interleukin-3 (IL-3), granulocyte-macrophage colony-stimulating factor, and IL-5 that leads to ligand independence and tumorigenicity

Blood ◽  
1994 ◽  
Vol 83 (10) ◽  
pp. 2802-2808 ◽  
Author(s):  
R D'Andrea ◽  
J Rayner ◽  
P Moretti ◽  
A Lopez ◽  
GJ Goodall ◽  
...  
Keyword(s):  
Large Family ◽  
Mutant Form ◽  
Sequence Motifs ◽  
Colony Stimulating Factor ◽  
Interleukin 5 ◽  
Interleukin 3 ◽  
Conserved Sequence ◽  
Macrophage Colony Stimulating Factor ◽  
Macrophage Colony ◽  
Stimulating Factor

Abstract The cytokines interleukin-3, interleukin-5, and granulocyte-macrophage colony-stimulating factor bind with high affinity to a receptor complex that contains a ligand-specific alpha-chain and a common beta-chain, h beta c. We report here the isolation of a mutant form of h beta c, from growth factor-independent cells, that arose spontaneously after infection of a murine factor-dependent hematopoietic cell line (FDC-P1) with a retroviral h beta c expression construct. Analysis of this h beta c mutation shows that a small (37 amino acid) duplication of extracellular sequence that includes two conserved sequence motifs is sufficient to confer ligand-independent growth on these cells and lead to tumourigenicity. Because this is a conserved region in the cytokine receptor superfamily, our results suggest that the large family of cytokine receptors has the capacity to become oncogenically active.

scholarly journals Identification of metalloprotease gene families in sugarcane

2001 ◽  
Vol 24 (1-4) ◽  
pp. 285-290 ◽  
Author(s):  
O.H.P. Ramos ◽  
H.S. Selistre-de-Araujo
Keyword(s):  
Expressed Sequence Tag ◽  
Gene Families ◽  
Data Bank ◽  
Matrix Metalloproteases ◽  
Sequence Motifs ◽  
Dna Library ◽  
Physiological Processes ◽  
Expressed Sequence ◽  
Enzyme Class

Metalloproteases play a key role in many physiological processes in mammals such as cell migration, tissue remodeling and processing of growth factors. They have also been identified as important factors in the patho-physiology of a number of human diseases, including cancer and hypertension. Many bacterial pathogens rely on proteases in order to infect the host. Several classes of metalloproteases have been described in humans, bacteria, snake venoms and insects. However, the presence and characterization of plant metalloproteases have rarely been described in the literature. In our research, we searched the sugarcane expressed sequence tag (SUCEST) DNA library in order to identify, by homology with sequences deposited in other databases, metalloprotease gene families expressed under different conditions. Protein sequences from Arabidopsis thaliana and Glycine max were used to search the SUCEST data bank. Conserved regions corresponding to different metalloprotease domains and sequence motifs were identified in the reads to characterize each group of enzymes. At least four classes of sugarcane metalloproteases have been identified, i.e. matrix metalloproteases, zincins, inverzincins, and ATP-dependent metalloproteases. Each enzyme class was analyzed for its expression in different conditions and tissues.

scholarly journals Identification, Evolutionary and Expression Analysis of PYL-PP2C-SnRK2s Gene Families in Soybean

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1356
Author(s):  
Zhaohan Zhang ◽  
Shahid Ali ◽  
Tianxu Zhang ◽  
Wanpeng Wang ◽  
Linan Xie
Keyword(s):  
Gene Family ◽  
Higher Plants ◽  
Expression Patterns ◽  
Family Members ◽  
Evolutionary Relationship ◽  
Gene Families ◽  
Class Iii ◽  
Sequencing Data ◽  
Entire Genome ◽  
Core Components

Abscisic acid (ABA) plays a crucial role in various aspects of plant growth and development, including fruit development and ripening, seed dormancy, and involvement in response to various environmental stresses. In almost all higher plants, ABA signal transduction requires three core components; namely, PYR/PYL/RCAR ABA receptors (PYLs), type 2C protein phosphatases (PP2Cs), and class III SNF-1-related protein kinase 2 (SnRK2s). The exploration of these three core components is not comprehensive in soybean. This study identified the GmPYL-PP2C-SnRK2s gene family members by using the JGI Phytozome and NCBI database. The gene family composition, conservation, gene structure, evolutionary relationship, cis-acting elements of promoter regions, and its coding protein domains were analyzed. In the entire genome of the soybean, there are 21 PYLs, 36 PP2Cs, and 21 SnRK2s genes; further, by phylogenetic and conservation analysis, 21 PYLs genes are classified into 3 groups, 36 PP2Cs genes are classified into seven groups, and 21 SnRK2s genes are classified into 3 groups. The conserved motifs and domain analysis showed that all the GmPYLs gene family members contain START-like domains, the GmPP2Cs gene family contains PP2Cc domains, and the GmSnRK2s gene family contains S_TK domains, respectively. Furthermore, based on the high-throughput transcriptome sequencing data, the results showed differences in the expression patterns of GmPYL-PP2C-SnRK2s gene families in different tissue parts of the same variety, and the same tissue part of different varieties. Our study provides a basis for further elucidation of the identification of GmPYL-PP2C-SnRK2s gene family members and analysis of their evolution and expression patterns, which helps to understand the molecular mechanism of soybean response to abiotic stress. In addition, this provides a conceptual basis for future studies of the soybean ABA core signal pathway.

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