Enhanced antimicrobial peptide-induced activity in the mollusc Toll-2 family through evolution via tandem Toll/interleukin-1 receptor

Toll receptors play an important role in the innate immunity of invertebrates. All reported Tolls have only one Toll/interleukin-1 receptor (TIR) domain at the C-terminal. In this study, numerous Tolls with tandem TIRs at the C-terminal were found in molluscs. Such Tolls presented an extra TIR (TIR-1) compared with Toll-I. Thus, Toll-I might be the ancestor of tandem TIRs containing Toll. To test this hypothesis, 83 Toll-I and Toll-2 (most have two TIRs, but others seem to be the evolutionary intermediates) genes from 29 shellfish species were identified. These Tolls were divided into nine groups based on phylogenetic analyses. A strong correlation between phylogeny and motif composition was found. All Toll proteins contained the TIR-2 domain, whereas the TIR-1 domain only existed in some Toll-2 protein, suggesting that TIR-1 domain insertion may play an important role in Toll protein evolution. Further analyses of functional divergence and adaptive evolution showed that some of the critical sites responsible for functional divergence may have been under positive selection. An additional intragenic recombination played an important role in the evolution of the Toll-I and Toll-2 genes. To investigate the functional difference of Toll-I and Toll-2, over expression of Hcu_Toll-I or Hcu_Toll-2-2 in Drosophila S2 cells was performed. Results showed that Hcu_Toll-2-2 had stronger antimicrobial peptide (AMP) activity than Hcu_Toll-I. Therefore, enhanced AMP-induced activity resulted from tandem TIRs in Toll-2s of molluscs during evolution history.

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Global Survey and Expressions of the Phosphate Transporter Gene Families in Brassica napus and Their Roles in Phosphorus Response

International Journal of Molecular Sciences ◽

10.3390/ijms21051752 ◽

2020 ◽

Vol 21 (5) ◽

pp. 1752 ◽

Cited By ~ 2

Author(s):

Jin Yang ◽

Jie Zhou ◽

Hong-Jun Zhou ◽

Mang-Mang Wang ◽

Ming-Ming Liu ◽

...

Keyword(s):

Brassica Napus ◽

Expression Profiles ◽

Phylogenetic Analyses ◽

Functional Divergence ◽

Gene Families ◽

Small Scale ◽

Transporter Gene ◽

Promoter Regions ◽

Network Analyses ◽

Group I

Phosphate (Pi) transporters play critical roles in Pi acquisition and homeostasis. However, currently little is known about these genes in oil crops. In this study, we aimed to characterize the five Pi transporter gene families (PHT1-5) in allotetraploid Brassica napus. We identified and characterized 81 putative PHT genes in B. napus (BnaPHTs), including 45 genes in PHT1 family (BnaPHT1s), four BnaPHT2s, 10 BnaPHT3s, 13 BnaPHT4s and nine BnaPHT5s. Phylogenetic analyses showed that the largest PHT1 family could be divided into two groups (Group I and II), while PHT4 may be classified into five, Groups I-V. Gene structure analysis revealed that the exon-intron pattern was conservative within the same family or group. The sequence characteristics of these five families were quite different, which may contribute to their functional divergence. Transcription factor (TF) binding network analyses identified many potential TF binding sites in the promoter regions of candidates, implying their possible regulating patterns. Collinearity analysis demonstrated that most BnaPHTs were derived from an allopolyploidization event (~40.7%) between Brassica rapa and Brassica oleracea ancestors, and small-scale segmental duplication events (~39.5%) in the descendant. RNA-Seq analyses proved that many BnaPHTs were preferentially expressed in leaf and flower tissues. The expression profiles of most colinearity-pairs in B. napus are highly correlated, implying functional redundancy, while a few pairs may have undergone neo-functionalization or sub-functionalization during evolution. The expression levels of many BnaPHTs tend to be up-regulated by different hormones inductions, especially for IAA, ABA and 6-BA treatments. qRT-PCR assay demonstrated that six BnaPHT1s (BnaPHT1.11, BnaPHT1.14, BnaPHT1.20, BnaPHT1.35, BnaPHT1.41, BnaPHT1.44) were significantly up-regulated under low- and/or rich- Pi conditions in B. napus roots. This work analyzes the evolution and expression of the PHT family in Brassica napus, which will help further research on their role in Pi transport.

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Calreticulin molecular evolution: a strong purifying and episodic diversifying selection result

Biologia ◽

10.2478/s11756-013-0327-7 ◽

2014 ◽

Vol 69 (3) ◽

Cited By ~ 3

Author(s):

Rigers Bakiu

Keyword(s):

Molecular Evolution ◽

Higher Plants ◽

Phylogenetic Analyses ◽

Purifying Selection ◽

Amino Acid Sequences ◽

Over Expression ◽

Diversifying Selection ◽

Pathological Conditions ◽

Weight Protein ◽

Low Molecular Weight Protein

AbstractCalreticulin (CRT) is a low molecular weight protein present in vertebrates, invertebrates and higher plants. Its multiple functions have been demonstrated. It plays an important role as a chaperone and Ca2+ buffer inside sarcoplasmic/endoplasmic reticulum (SR/ER), and outside the ER in many physiological/pathological processes. Recently it has been observed that CRT over-expression or its absence is linked to various pathological conditions, such as malignant evolution and progression, and these facts really increased its study interests. Using an evolution approach CRT was further characterized. Several Bayesian phylogenetic analyses were performed using coding and amino acid sequences. CRT molecular evolution was investigated for the presence of negative or/and positive selection using HyPhy package. The results indicated that the purifying selection might have operated over the whole CRT primary structure. Although, an episodic diversifying selection was also found on the analyzed CRT sequences.

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Adenovirus-mediated over-expression of Interleukin-1 receptor antagonist reduces susceptibility to excitotoxic brain injury in perinatal rats

Neuroscience ◽

10.1016/0306-4522(96)00225-4 ◽

1996 ◽

Vol 75 (4) ◽

pp. 1033-1045 ◽

Cited By ~ 52

Author(s):

P Hagan ◽

J.D.E Barks ◽

M Yabut ◽

B.L Davidson ◽

B Roessler ◽

...

Keyword(s):

Brain Injury ◽

Receptor Antagonist ◽

Interleukin 1 ◽

Over Expression ◽

Interleukin 1 Receptor Antagonist

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Recurrent functional divergence of early tetrapod keratins in amphibian toe pads and mammalian hair

Biology Letters ◽

10.1098/rsbl.2013.0051 ◽

2013 ◽

Vol 9 (3) ◽

pp. 20130051 ◽

Cited By ~ 10

Author(s):

Wim Vandebergh ◽

Margo Maex ◽

Franky Bossuyt ◽

Ines Van Bocxlaer

Keyword(s):

Cdna Library ◽

Phylogenetic Analyses ◽

Functional Divergence ◽

Cytoskeletal Proteins ◽

Evolutionary Origin ◽

Structural Proteins ◽

Tree Frog ◽

Hyla Cinerea ◽

Early Tetrapods ◽

Mammalian Hair

Amphibians have invaded arboreal habitats multiple times independently during their evolution. Adaptation to these habitats was nearly always accompanied by the presence or appearance of toe pads, flattened enlargements on tips of fingers and toes that provide adhesive power in these environments. The strength and elasticity of the toe pad relies on polygonal arrayed cells ending in nanoscale projections, which are densely packed with cytoskeletal proteins. Here, we characterized and determined the evolutionary origin of these proteins in the toe pad of the tree frog Hyla cinerea . We created a subtracted cDNA library enriching genes that are expressed in the toe pad, but nowhere else in the toe. Our analyses revealed five alpha keratins as main structural proteins of the amphibian toe pad. Phylogenetic analyses show that these proteins belong to different keratin lineages that originated in an early tetrapod ancestor and in mammals evolved to become the major keratin types of hair. The ancestral keratins were probably already expressed in areas that required skin reinforcement in early tetrapods, and subsequently diverged to support fundamentally different adaptive structures in amphibians and mammals.

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Phylogenetic analyses reveal molecular signatures associated with functional divergence among Subtilisin like Serine Proteases are linked to lifestyle transitions in Hypocreales

BMC Evolutionary Biology ◽

10.1186/s12862-016-0793-y ◽

2016 ◽

Vol 16 (1) ◽

Cited By ~ 6

Author(s):

Deepti Varshney ◽

Akanksha Jaiswar ◽

Alok Adholeya ◽

Pushplata Prasad

Keyword(s):

Serine Proteases ◽

Phylogenetic Analyses ◽

Functional Divergence ◽

Molecular Signatures

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Extended insight into the preponderance of LRRs - a docking & simulation study with members of the TLR1 subfamily

10.1101/592626 ◽

2019 ◽

Author(s):

Debayan Dey ◽

Dipanjana Dhar ◽

Sucharita Das ◽

Aditi Maulik ◽

Soumalee Basu

Keyword(s):

Phylogenetic Analyses ◽

Interleukin 1 ◽

Docking Simulation ◽

Md Simulations ◽

Structural Motif ◽

Cellular Processes ◽

Binding Function ◽

C Terminus ◽

Evolutionarily Conserved ◽

Leucine Rich Repeats

AbstractThe widespread structural motif of Leucine-rich repeats (LRR) constitute the extracellular part of the Toll-like receptor (TLR) family preceded by an intracellular Toll/interleukin-1 receptor (TIR) domain at the C-terminus. The benefit of using LRRs in these pattern recognition receptors (PRR) that are responsible for early detection of pathogens to elicit inflammatory/innate immune response still remains elusive. Phylogenetic analyses (Maximum Likelihood and Bayesian Inference) of nine TLR (TLR 1-9) genes from 36 mammals reconfirmed the existence of two distinct clades, one (TLR1/2/6) for recognizing bacterial cell wall derivatives and another (TLR7/8/9) for various nucleic acids. TLR3, TLR4 and TLR5 showed independent line of evolution. The distinction of the TLR1 subfamily to form heterodimers within its members and the existence of the paralogs TLR1 and TLR6 therein, was appealing enough to carry out further studies with the extracellular recognition domain. Dimerizing and ligand binding residues from the crystal structures of TLR1 and TLR6 were interchanged to generate chimeric proteins. The dimer forming ability of these variants with their common partner, TLR2, were checked before running MD simulations. The chimeras were compared with wild type dimers to find no significant alterations in the overall structure. Finally, interchanged ligands were docked to the variants to ratify reversal of the binding function. Intriguingly, sequence change in substantial numbers, 16 in TLR1 and 18 in TLR6, preserves the native scaffold offered by LRRs. This exercise thus depicts how the LRR motif has been advantageous to be selected as an evolutionarily conserved motif for essential cellular processes.

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Altered fungal sensitivity to a plant antimicrobial peptide through over-expression of yeast cDNAs

Current Genetics ◽

10.1007/s00294-005-0562-8 ◽

2005 ◽

Vol 47 (3) ◽

pp. 194-201 ◽

Cited By ~ 12

Author(s):

Camilla Stephens ◽

Stuart J. Harrison ◽

Kemal Kazan ◽

Frank W. N. Smith ◽

Ken C. Goulter ◽

...

Keyword(s):

Antimicrobial Peptide ◽

Over Expression

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Letea Virus: Comparative Genomics and Phylogenetic Analysis of a Novel Reassortant Orbivirus Discovered in Grass Snakes (Natrix natrix)

Viruses ◽

10.3390/v12020243 ◽

2020 ◽

Vol 12 (2) ◽

pp. 243 ◽

Cited By ~ 3

Author(s):

Alexandru Tomazatos ◽

Rachel E. Marschang ◽

Iulia Maranda ◽

Heike Baum ◽

Alexandra Bialonski ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Sand Fly ◽

Intragenic Recombination ◽

Surveillance Program ◽

Biting Midges ◽

Natrix Natrix ◽

New Information ◽

Gene Reassortment ◽

Virus Strains

The discovery and characterization of novel arthropod-borne viruses provide valuable information on their genetic diversity, ecology, evolution and potential to threaten animal or public health. Arbovirus surveillance is not conducted regularly in Romania, being particularly very scarce in the remote and diverse areas like the Danube Delta. Here we describe the detection and genetic characterization of a novel orbivirus (Reoviridae: Orbivirus) designated as Letea virus, which was found in grass snakes (Natrix natrix) during a metagenomic and metatranscriptomic survey conducted between 2014 and 2017. This virus is the first orbivirus discovered in reptiles. Phylogenetic analyses placed Letea virus as a highly divergent species in the Culicoides-/sand fly-borne orbivirus clade. Gene reassortment and intragenic recombination were detected in the majority of the nine Letea virus strains obtained, implying that these mechanisms play important roles in the evolution and diversification of the virus. However, the screening of arthropods, including Culicoides biting midges collected within the same surveillance program, tested negative for Letea virus infection and could not confirm the arthropod vector of the virus. The study provided complete genome sequences for nine Letea virus strains and new information about orbivirus diversity, host range, ecology and evolution. The phylogenetic associations warrant further screening of arthropods, as well as sustained surveillance efforts for elucidation of Letea virus natural cycle and possible implications for animal and human health.

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