scholarly journals Gene conversions are frequent but not under positive selection in the Siglec gene families of primates

Genome ◽  
2014 ◽  
Vol 57 (6) ◽  
pp. 317-325 ◽  
Author(s):  
Mouldi Zid ◽  
Guy Drouin
Keyword(s):  
Sequence Similarity ◽  
Purifying Selection ◽  
Gene Families ◽  
Surface Proteins ◽  
Primate Species ◽  
Immunoglobulin Superfamily ◽  
Sialic Acid Binding ◽  
High Degree ◽  
Gene Conversions

Siglecs are cell surface proteins that belong to the immunoglobulin superfamily and which bind sialic acids. They are composed of two groups, the conserved Siglecs and the CD33-related Siglecs. Previous studies have reported the occurrence of gene conversions between human CD33-related Siglecs and suggested that these conversions are adaptive because they increase the diversity of these immunoglobulin-related genes. Here, we analyze the Siglec genes of five primate species and show that gene conversions are not observed between conserved Siglec genes but that they are frequent between primate CD33-related Siglecs. The gene conversions between CD33-related Siglec genes only occur between similar genes and equally frequently in sialic acid binding and nonbinding domains. Furthermore, dN/dS ratio tests show that most of the Ig-like V-type 1 and the Ig-like C2-type 1 domains of Siglec genes evolve either neutrally or under purifying selection and that gene conversions were not responsible for the positively selected regions detected in the Ig-like V-type1 domain of the human SIGLEC7 and SIGLEC9 genes. Our results suggest that the frequent gene conversions between CD33-related Siglec genes are simply a consequence of the high degree of sequence similarity of these genes and that they are not adaptive.

mSiglec-E, a novel mouse CD33-related siglec (sialic acid-binding immunoglobulin-like lectin) that recruits Src homology 2 (SH2)-domain-containing protein tyrosine phosphatases SHP-1 and SHP-2

2001 ◽  
Vol 353 (3) ◽  
pp. 483-492 ◽  
Author(s):  
Zhenbao YU ◽  
Meryem MAOUI ◽  
Liangtang WU ◽  
Denis BANVILLE ◽  
Shi-Hsiang SHEN
Keyword(s):  
Sialic Acid ◽  
Sequence Similarity ◽  
Tyrosine Phosphatase ◽  
Protein Tyrosine Phosphatases ◽  
Sh2 Domain ◽  
Immunoglobulin Superfamily ◽  
Protein Tyrosine ◽  
Src Homology 2 ◽  
Sialic Acid Binding ◽  
Src Homology

The sialic acid-binding immunoglobulin-like lectins (siglecs) represent a recently defined distinct subset of the immunoglobulin superfamily. By using the Src homology 2 (SH2)-domain-containing protein tyrosine phosphatase SHP-1 as bait in a yeast two-hybrid screen, we have identified a new member of the mouse siglec family, mSiglec-E. The mSiglec-E cDNA encodes a protein of 467 amino acids that contains three extracellular immunoglobulin-like domains, a transmembrane region and a cytoplasmic tail bearing two immunoreceptor tyrosine-based inhibitory motifs (ITIMs). mSiglec-E is highly expressed in mouse spleen, a tissue rich in leucocytes. The ITIMs of mSiglec-E can recruit SHP-1 and SHP-2, two inhibitory regulators of immunoreceptor signal transduction. This suggests that the function of mSiglec-E is probably an involvement in haematopoietic cells and the immune system as an inhibitory receptor. When expressed in COS-7 cells, mSiglec-E was able to mediate sialic acid-dependent binding to human red blood cells, suggesting that mSiglec-E may function through cell–cell interactions. In comparison with the known members of the siglec family, mSiglec-E exhibits a high degree of sequence similarity to both human siglec-7 and siglec-9. The gene encoding mSiglec-E is localized in the same chromosome as that encoding mouse CD33. Phylogenetic analysis reveals that neither mouse mSiglec-E nor CD33 shows a clear relationship with any human siglecs so far identified.

Identification, characterization and leucocyte expression of Siglec-10, a novel human sialic acid-binding receptor

2001 ◽  
Vol 355 (2) ◽  
pp. 489-497 ◽  
Author(s):  
James MUNDAY ◽  
Sheena KERR ◽  
Jian NI ◽  
Ann L. CORNISH ◽  
Jiquan Q. ZHANG ◽  
...  
Keyword(s):  
Sialic Acid ◽  
Innate Immune System ◽  
Sequence Similarity ◽  
Innate Immune ◽  
Inhibitory Receptor ◽  
Human Spleen ◽  
Minor Population ◽  
Sialic Acid Binding ◽  
A Minor ◽  
High Degree

Here we characterize Siglec-10 as a new member of the Siglec family of sialic acid-binding Ig-like lectins. A full-length cDNA was isolated from a human spleen library and the corresponding gene identified. Siglec-10 is predicted to contain five extracellular Ig-like domains and a cytoplasmic tail containing three putative tyrosine-based signalling motifs. Siglec-10 exhibited a high degree of sequence similarity to CD33-related Siglecs and mapped to the same region, on chromosome 19q13.3. The expressed protein was able to mediate sialic acid-dependent binding to human erythrocytes and soluble sialoglycoconjugates. Using specific antibodies, Siglec-10 was detected on subsets of human leucocytes including eosinophils, monocytes and a minor population of natural killer-like cells. The molecular properties and expression pattern suggest that Siglec-10 may function as an inhibitory receptor within the innate immune system.

scholarly journals The BBA01 Protein, a Member of Paralog Family 48 from Borrelia burgdorferi, Is Potentially Interchangeable with the Channel-Forming Protein P13

2006 ◽  
Vol 188 (12) ◽  
pp. 4207-4217 ◽  
Author(s):  
Marija Pinne ◽  
Katrin Denker ◽  
Elin Nilsson ◽  
Roland Benz ◽  
Sven Bergström
Keyword(s):  
Borrelia Burgdorferi ◽  
Single Channel ◽  
Sequence Similarity ◽  
Shuttle Vector ◽  
Protein A ◽  
Gene Families ◽  
Wild Type ◽  
C Terminus ◽  
High Degree ◽  
Paralog Family

ABSTRACT The Borrelia burgdorferi genome exhibits redundancy, with many plasmid-carried genes belonging to paralogous gene families. It has been suggested that certain paralogs may be necessary in various environments and that they are differentially expressed in response to different conditions. The chromosomally located p13 gene which codes for a channel-forming protein belongs to paralog family 48, which consists of eight additional genes. Of the paralogous genes from family 48, the BBA01 gene has the highest homology to p13. Herein, we have inactivated the BBA01 gene in B. burgdorferi strain B31-A. This mutant shows no apparent phenotypic difference compared to the wild type. However, analysis of BBA01 in a C-terminal protease A (CtpA)-deficient background revealed that like P13, BBA01 is posttranslationally processed at its C terminus. Elevated BBA01 expression was obtained in strains with the BBA01 gene introduced on the shuttle vector compared to the wild-type strain. We could further demonstrate that BBA01 is a channel-forming protein with properties surprisingly similar to those of P13. The single-channel conductance, of about 3.5 nS, formed by BBA01 is comparable to that of P13, which together with the high degree of sequence similarity suggests that the two proteins may have similar and interchangeable functions. This is further strengthened by the up-regulation of the BBA01 protein and its possible localization in the outer membrane in a p13 knockout strain, thus suggesting that P13 can be replaced by BBA01.

Stronger purifying selection against gene conversions in a pathogenicSaccharomyces cerevisiaestrain

Genome ◽  
2012 ◽  
Vol 55 (12) ◽  
pp. 835-843
Author(s):  
Benoît Pagé ◽  
Guy Drouin
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Gene Family ◽  
Purifying Selection ◽  
Gene Families ◽  
Lower Number ◽  
Pathogenic Strain ◽  
Helicase Gene ◽  
Nonpathogenic Strain ◽  
S288c Strain ◽  
Gene Conversions

Gene conversions most often have no selective impact, but some are selectively disadvantageous whereas others are selectively advantageous. Although gene conversions have been extensively studied in yeasts, very little is known about their selective impact in pathological yeasts. Here, we used the GENECONV software to compare the characteristics of candidate gene conversions found in a pathogenic strain (YJM789) and a nonpathogenic strain (S288c) of Saccharomyces cerevisiae. Interestingly, the pathogenic strain has fewer gene conversions when compared with the nonpathogenic strain. Of the 123 conversions we identified, 27 were identical or similar between the two strains, 62 were specific to the S288c strain, and 34 were specific to the YJM789 strain. Identical and similar conversions likely represent conversions that are under similar levels of purifying selection in both strains. The lower number of gene conversions in most gene families of the pathogenic strain is likely the result of higher purifying selection in this strain. In contrast, the higher number of conversions found in the YRF1 helicase gene family of the pathogenic strain could represent an example of adaptive gene conversions involved in maintaining its telomeres.

scholarly journals Novel Member of the CD209 (DC-SIGN) Gene Family in Primates

2003 ◽  
Vol 77 (1) ◽  
pp. 217-227 ◽  
Author(s):  
Arman A. Bashirova ◽  
Li Wu ◽  
Jie Cheng ◽  
Thomas D. Martin ◽  
Maureen P. Martin ◽  
...  
Keyword(s):  
Gene Family ◽  
Sequence Similarity ◽  
Primate Species ◽  
Axillary Lymph Nodes ◽  
Target Cells ◽  
Axillary Lymph ◽  
Functional Activities ◽  
High Level

ABSTRACT Two CD209 family genes identified in humans, CD209 (DC-SIGN) and CD209L (DC-SIGNR/L-SIGN), encode C-type lectins that serve as adhesion receptors for ICAM-2 and ICAM-3 and participate in the transmission of human and simian immunodeficiency viruses (HIV and SIV, respectively) to target cells in vitro. Here we characterize the CD209 gene family in nonhuman primates and show that recent evolutionary alterations have occurred in this family across primate species. All of the primate species tested, specifically, Old World monkeys (OWM) and apes, have orthologues of human CD209. In contrast, CD209L is missing in OWM but present in apes. A third family member, that we have named CD209L2, was cloned from rhesus monkey cDNA and subsequently identified in OWM and apes but not in humans. Rhesus CD209L2 mRNA was prominently expressed in the liver and axillary lymph nodes, although preliminary data suggest that levels of expression may vary among individuals. Despite a high level of sequence similarity to both human and rhesus CD209, rhesus CD209L2 was substantially less effective at binding ICAM-3 and poorly transmitted HIV type 1 and SIV to target cells relative to CD209. Our data suggest that the CD209 gene family has undergone recent evolutionary processes involving duplications and deletions, the latter of which may be tolerated because of potentially redundant functional activities of the molecules encoded by these genes.

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.

Differential regulation of glucose transporter isoforms by the src oncogene in chicken embryo fibroblasts

1991 ◽  
Vol 11 (9) ◽  
pp. 4448-4454
Author(s):  
M K White ◽  
T B Rall ◽  
M J Weber
Keyword(s):  
Glucose Transport ◽  
Chicken Embryo ◽  
Glucose Transporter ◽  
Sequence Similarity ◽  
Transporter Protein ◽  
Mrna Induction ◽  
Embryo Fibroblasts ◽  
Type 3 ◽  
Chicken Embryo Fibroblasts

The increase in glucose transport that occurs when chicken embryo fibroblasts (CEFs) are transformed by src is associated with an increase in the amount of type 1 glucose transporter protein, and we have previously shown that this effect is due to a decrease in the degradation rate of this protein. The rate of CEF type 1 glucose transporter biosynthesis and the level of its mRNA are unaffected by src transformation. To study the molecular basis of this phenomenon, we have been isolating chicken glucose transporter cDNAs by hybridization to a rat type 1 glucose transporter probe at low stringency. Surprisingly, these clones corresponded to a message encoding a protein which has most sequence similarity to the human type 3 glucose transporter and which we refer to as CEF-GT3. CEF-GT3 is clearly distinct from the CEF type 1 transporter that we have previously described. Northern (RNA) analysis of CEF RNA with CEF-GT3 cDNA revealed two messages of 1.7 and 3.3 kb which were both greatly induced by src transformation. When the CEF-GT3 cDNA was expressed in rat fibroblasts, a three-to fourfold enhancement of 2-deoxyglucose uptake was observed, indicating that CEF-GT3 is a functional glucose transporter. Northern analyses using a CEF-GT3 and a rat type 1 probe demonstrated that there is no hybridization between different isoforms but that there is cross-species hybridization between the rat type 1 probe and the chicken homolog. Southern blot analyses confirmed that the chicken genomic type 1 and type 3 transporters are encoded by distinct genes. We conclude that CEFs express two types of transporter, type 1 (which we have previously reported to be regulated posttranslationally by src) and a novel type 3 isoform which, unlike type 1, shows mRNA induction upon src transformation. We conclude that src regulates glucose transport in CEFs simultaneously by two different mechanisms.

Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements

2021 ◽  
pp. gr.275658.121
Author(s):  
Yuyun Zhang ◽  
Zijuan Li ◽  
Yu'e Zhang ◽  
Kande Lin ◽  
Yuan Peng ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Genome Evolution ◽  
Regulatory Networks ◽  
Transcriptional Regulatory Network ◽  
Sequence Similarity ◽  
Purifying Selection ◽  
Wheat Genome ◽  
Specific Gene ◽  
High Sequence Similarity ◽  
Wheat Genome Evolution

More than 80% of the wheat genome consists of transposable elements (TEs), which act as one major driver of wheat genome evolution. However, their contributions to the regulatory evolution of wheat adaptations remain largely unclear. Here, we created genome-binding maps for 53 transcription factors (TFs) underlying environmental responses by leveraging DAP-seq in Triticum urartu, together with epigenomic profiles. Most TF-binding sites (TFBS) located distally from genes are embedded in TEs, whose functional relevance is supported by purifying selection and active epigenomic features. About 24% of the non-TE TFBS share significantly high sequence similarity with TE-embedded TFBS. These non-TE TFBS have almost no homologous sequences in non-Triticeae species and are potentially derived from Triticeae-specific TEs. The expansion of TE-derived TFBS linked to wheat-specific gene responses, suggesting TEs are an important driving force for regulatory innovations. Altogether, TEs have been significantly and continuously shaping regulatory networks related to wheat genome evolution and adaptation.

scholarly journals Characterization and Transcript Profiling of PME and PMEI Gene Families during Peach Fruit Maturation

2017 ◽  
Vol 142 (4) ◽  
pp. 246-259 ◽  
Author(s):  
Yunqing Zhu ◽  
Wenfang Zeng ◽  
Xiaobei Wang ◽  
Lei Pan ◽  
Liang Niu ◽  
...  
Keyword(s):  
Fruit Ripening ◽  
Prunus Persica ◽  
Expression Patterns ◽  
Pectin Methylesterase ◽  
Gene Families ◽  
Naphthaleneacetic Acid ◽  
Regulation Mechanism ◽  
Fruit Softening ◽  
Peach Fruit

Pectins are synthesized and secreted to the cell wall as highly methyl-esterified polymers and demethyl-esterified by pectin methylesterases (PMEs), which are regulated by pectin methylesterase inhibitors (PMEIs). PMEs and PMEIs are involved in pectin degradation during fruit softening; however, the roles of the PME and PMEI gene families during fruit softening remain unclear. Here, 71 PME and 30 PMEI genes were identified in the peach (Prunus persica) genome and shown to be unevenly distributed on all eight chromosomes. The 71 PME genes comprised 36 Type-1 PMEs and 35 Type-2 PMEs. Transcriptome analysis showed that 11 PME and 15 PMEI genes were expressed during fruit ripening in melting flesh (MF) and stony-hard (SH) peaches. Three PME and five PMEI genes were expressed at higher levels in MF than in SH fruit and exhibited softening-associated expression patterns. Upstream regulatory cis elements of these genes related to hormone response, especially naphthaleneacetic acid and ethylene, were investigated. One PME (Prupe.7G192800) and two PMEIs (Prupe.1G114500 and Prupe.2G279800), and their promoters were identified as potential targets for future studies on the biochemical metabolism and regulation of fruit ripening. The comprehensive data generated in this study will improve our understanding of the PME and PMEI gene families in peach. However, further detailed investigation is necessary to elucidate the biochemical function and regulation mechanism of the PME and PMEI genes during peach fruit ripening.

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