scholarly journals The MHC Class Ia Genes in Chenfu’s Treefrog (Zhangixalus chenfui) Evolved via Gene Duplication, Recombination, and Selection

Animals ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 34
Author(s):  
Hu Chen ◽  
Siqi Huang ◽  
Ye Jiang ◽  
Fuyao Han ◽  
Qingyong Ni ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Positive Selection ◽  
Phylogenetic Relationships ◽  
Molecular Mechanisms ◽  
Coding Region ◽  
Evolutionary Mechanisms ◽  
Evolutionary Patterns ◽  
Mhc Genes ◽  
Mhc Class Ia ◽  
Related Proteins

The molecular mechanisms underlying the evolution of adaptive immunity-related proteins can be deduced by a thorough examination of the major histocompatibility complex (MHC). Currently, in vertebrates, there is a relatively large amount of research on MHCs in mammals and birds. However, research related to amphibian MHC genes and knowledge about the evolutionary patterns is limited. This study aimed to isolate the MHC class I genes from Chenfu’s Treefrog (Zhangixalus chenfui) and reveal the underlying evolutionary processes. A total of 23 alleles spanning the coding region of MHC class Ia genes were identified in 13 individual samples. Multiple approaches were used to test and identify recombination from the 23 alleles. Amphibian MHC class Ia alleles, from NCBI, were used to construct the phylogenetic relationships in MEGA. Additionally, the partition strategy was adopted to construct phylogenetic relationships using MrBayes and MEGA. The sites of positive selection were identified by FEL, PAML, and MEME. In Chenfu’s Treefrog, we found that: (1) recombination usually takes place between whole exons of MHC class Ia genes; (2) there are at least 3 loci for MHC class Ia, and (3) the diversity of genes in MHC class Ia can be attributed to recombination, gene duplication, and positive selection. We characterized the evolutionary mechanisms underlying MHC class Ia genes in Chenfu’s Treefrog, and in so doing, broadened the knowledge of amphibian MHC systems.

scholarly journals Contrasting Patterns of Gene Duplication, Relocation, and Selection Among Human Taste Genes

2021 ◽  
Vol 17 ◽  
pp. 117693432110351
Author(s):  
Yupeng Wang ◽  
Ying Sun ◽  
Paule Valery Joseph
Keyword(s):  
Gene Duplication ◽  
Gene Family ◽  
Functional Groups ◽  
Purifying Selection ◽  
Comparative Genomic ◽  
Vertebrate Species ◽  
Evolutionary Mechanisms ◽  
Evolutionary Patterns ◽  
Outgroup Species ◽  
Tandem Duplications

In humans, taste genes are responsible for perceiving at least 5 different taste qualities. Human taste genes’ evolutionary mechanisms need to be explored. We compiled a list of 69 human taste-related genes and divided them into 7 functional groups. We carried out comparative genomic and evolutionary analyses for these taste genes based on 8 vertebrate species. We found that relative to other groups of human taste genes, human TAS2R genes have a higher proportion of tandem duplicates, suggesting that tandem duplications have contributed significantly to the expansion of the human TAS2R gene family. Human TAS2R genes tend to have fewer collinear genes in outgroup species and evolve faster, suggesting that human TAS2R genes have experienced more gene relocations. Moreover, human TAS2R genes tend to be under more relaxed purifying selection than other genes. Our study sheds new insights into diverse and contrasting evolutionary patterns among human taste genes.

scholarly journals Progress in understanding the role of lncRNA in programmed cell death

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Na Jiang ◽  
Xiaoyu Zhang ◽  
Xuejun Gu ◽  
Xiaozhuang Li ◽  
Lei Shang
Keyword(s):  
Cell Death ◽  
Programmed Cell Death ◽  
Molecular Mechanisms ◽  
Membrane Receptors ◽  
Gene Expressions ◽  
Apoptosis Pathway ◽  
Stem Cell Pluripotency ◽  
Extrinsic Apoptosis ◽  
Related Proteins ◽  
Cycle Regulation

AbstractLong non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides but not translated into proteins. LncRNAs regulate gene expressions at multiple levels, such as chromatin, transcription, and post-transcription. Further, lncRNAs participate in various biological processes such as cell differentiation, cell cycle regulation, and maintenance of stem cell pluripotency. We have previously reported that lncRNAs are closely related to programmed cell death (PCD), which includes apoptosis, autophagy, necroptosis, and ferroptosis. Overexpression of lncRNA can suppress the extrinsic apoptosis pathway by downregulating of membrane receptors and protect tumor cells by inhibiting the expression of necroptosis-related proteins. Some lncRNAs can also act as competitive endogenous RNA to prevent oxidation, thereby inhibiting ferroptosis, while some are known to activate autophagy. The relationship between lncRNA and PCD has promising implications in clinical research, and reports have highlighted this relationship in various cancers such as non-small cell lung cancer and gastric cancer. This review systematically summarizes the advances in the understanding of the molecular mechanisms through which lncRNAs impact PCD.

scholarly journals Divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus

2021 ◽  
Author(s):  
Zhilin Yuan ◽  
Irina S. Druzhinina ◽  
John G. Gibbons ◽  
Zhenhui Zhong ◽  
Yves Van de Peer ◽  
...  
Keyword(s):  
Membrane Trafficking ◽  
Molecular Mechanisms ◽  
Genomic Island ◽  
Population Genomics ◽  
Growth Yield ◽  
Fixation Index ◽  
Nucleotide Polymorphisms ◽  
Evolutionary Mechanisms ◽  
Melanin Biosynthesis ◽  
Two Populations

AbstractUnderstanding how organisms adapt to extreme living conditions is central to evolutionary biology. Dark septate endophytes (DSEs) constitute an important component of the root mycobiome and they are often able to alleviate host abiotic stresses. Here, we investigated the molecular mechanisms underlying the beneficial association between the DSE Laburnicola rhizohalophila and its host, the native halophyte Suaeda salsa, using population genomics. Based on genome-wide Fst (pairwise fixation index) and Vst analyses, which compared the variance in allele frequencies of single-nucleotide polymorphisms (SNPs) and copy number variants (CNVs), respectively, we found a high level of genetic differentiation between two populations. CNV patterns revealed population-specific expansions and contractions. Interestingly, we identified a ~20 kbp genomic island of high divergence with a strong sign of positive selection. This region contains a melanin-biosynthetic polyketide synthase gene cluster linked to six additional genes likely involved in biosynthesis, membrane trafficking, regulation, and localization of melanin. Differences in growth yield and melanin biosynthesis between the two populations grown under 2% NaCl stress suggested that this genomic island contributes to the observed differences in melanin accumulation. Our findings provide a better understanding of the genetic and evolutionary mechanisms underlying the adaptation to saline conditions of the L. rhizohalophila–S. salsa symbiosis.

scholarly journals Molecular evolution of dengue virus types 1 and 4 in Korean travelers

2021 ◽  
Vol 166 (4) ◽  
pp. 1103-1112
Author(s):  
Eun-Ha Hwang ◽  
Green Kim ◽  
Hoyin Chung ◽  
Hanseul Oh ◽  
Jong-Hwan Park ◽  
...  
Keyword(s):  
Dengue Virus ◽  
Positive Selection ◽  
Recent Common Ancestor ◽  
Coding Region ◽  
Genotype I ◽  
Most Recent Common Ancestor ◽  
Evolutionary Features ◽  
Molecular Phylogenetic ◽  
First Time ◽  
Global Travel

AbstractDengue virus (DV) is a mosquito-borne virus that is endemic to many tropical and subtropical areas. Recently, the annual incidence of DV infection has increased worldwide, including in Korea, due to global warming and increased global travel. We therefore sought to characterize the molecular and evolutionary features of DV-1 and DV-4 isolated from Korean overseas travelers. We used phylogenetic analysis based on the full coding region to classify isolates of DV-1 in Korea into genotype I (43251, KP406802), genotype IV (KP406803), and genotype V (KP406801). In addition, we found that strains of DV-4 belonged to genotype I (KP406806) and genotype II (43257). Evidence of positive selection in DV-1 strains was identified in the C, prM, NS2A, and NS5 proteins, whereas DV-4 showed positive selection only in the non-structural proteins NS2A, NS3, and NS5. The substitution rates per site per year were 5.58 × 10-4 and 6.72 × 10-4 for DV-1 and DV-4, respectively, and the time of the most recent common ancestor was determined using the Bayesian skyline coalescent method. In this study, the molecular, phylogenetic, and evolutionary characteristics of Korean DV-1 and DV-4 isolates were evaluated for the first time.

Parallel molecular mechanisms for enzyme temperature adaptation

Science ◽  
2021 ◽  
Vol 371 (6533) ◽  
pp. eaay2784
Author(s):  
Margaux M. Pinney ◽  
Daniel A. Mokhtari ◽  
Eyal Akiva ◽  
Filip Yabukarski ◽  
David M. Sanchez ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Interaction Networks ◽  
Temperature Adaptation ◽  
Mechanistic Studies ◽  
Sequence Analyses ◽  
Evolutionary Mechanisms ◽  
Ketosteroid Isomerase ◽  
Physical Mechanisms ◽  
Bacterial Enzyme ◽  
Enzyme Families

The mechanisms that underly the adaptation of enzyme activities and stabilities to temperature are fundamental to our understanding of molecular evolution and how enzymes work. Here, we investigate the molecular and evolutionary mechanisms of enzyme temperature adaption, combining deep mechanistic studies with comprehensive sequence analyses of thousands of enzymes. We show that temperature adaptation in ketosteroid isomerase (KSI) arises primarily from one residue change with limited, local epistasis, and we establish the underlying physical mechanisms. This residue change occurs in diverse KSI backgrounds, suggesting parallel adaptation to temperature. We identify residues associated with organismal growth temperature across 1005 diverse bacterial enzyme families, suggesting widespread parallel adaptation to temperature. We assess the residue properties, molecular interactions, and interaction networks that appear to underly temperature adaptation.

scholarly journals Restricting nonclassical MHC genes coevolve with TRAV genes used by innate-like T cells in mammals

2016 ◽  
Vol 113 (21) ◽  
pp. E2983-E2992 ◽  
Author(s):  
Pierre Boudinot ◽  
Stanislas Mondot ◽  
Luc Jouneau ◽  
Luc Teyton ◽  
Marie-Paule Lefranc ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Purifying Selection ◽  
Cell Receptor ◽  
Nkt Cells ◽  
Evolutionary Patterns ◽  
Mait Cells ◽  
Mhc Genes ◽  
Class 1 ◽  
Complementarity Determining Regions

Whereas major histocompatibility class-1 (MH1) proteins present peptides to T cells displaying a large T-cell receptor (TR) repertoire, MH1Like proteins, such as CD1D and MR1, present glycolipids and microbial riboflavin precursor derivatives, respectively, to T cells expressing invariant TR-α (iTRA) chains. The groove of such MH1Like, as well as iTRA chains used by mucosal-associated invariant T (MAIT) and natural killer T (NKT) cells, respectively, may result from a coevolution under particular selection pressures. Herein, we investigated the evolutionary patterns of the iTRA of MAIT and NKT cells and restricting MH1Like proteins: MR1 appeared 170 Mya and is highly conserved across mammals, evolving more slowly than other MH1Like. It has been pseudogenized or independently lost three times in carnivores, the armadillo, and lagomorphs. The corresponding TRAV1 gene also evolved slowly and harbors highly conserved complementarity determining regions 1 and 2. TRAV1 is absent exclusively from species in which MR1 is lacking, suggesting that its loss released the purifying selection on MR1. In the rabbit, which has very few NKT and no MAIT cells, a previously unrecognized iTRA was identified by sequencing leukocyte RNA. This iTRA uses TRAV41, which is highly conserved across several groups of mammals. A rabbit MH1Like gene was found that appeared with mammals and is highly conserved. It was independently lost in a few groups in which MR1 is present, like primates and Muridae, illustrating compensatory emergences of new MH1Like/Invariant T-cell combinations during evolution. Deciphering their role is warranted to search similar effector functions in humans.

scholarly journals Ecology and biology of chemoreception in polychaetes

Zoosymposia ◽  
2009 ◽  
Vol 2 (1) ◽  
pp. 339-367 ◽  
Author(s):  
SARA M. LINDSAY
Keyword(s):  
Nervous System ◽  
Confocal Microscopy ◽  
Phylogenetic Relationships ◽  
Laser Scanning ◽  
Molecular Mechanisms ◽  
Laser Scanning Confocal Microscopy ◽  
Marine Organisms ◽  
Sensory Structure ◽  
Scanning Confocal Microscopy ◽  
Morphological Studies

Nervous system and sensory structure morphologies provide useful information for reconstructing phylogenetic relationships among the Polychaeta, Annelida, and Arthropoda. With the more common use of indirect immunocytochemistry and laser scanning confocal microscopy methods, the detailed information available from morphological studies has increased. Despite this wealth of information, developing an integrated understanding of the ecology, physiology, morphology, and molecular mechanisms of sensory systems in polychaetes remains a challenge.      For many marine organisms, including polychaetes, chemical signals and chemoreception mediate numerous ecologically important behaviors including defense, reproduction, recruitment, and feeding, yet the mechanism of chemoreception in polychaetes has not been well described. This review summarizes research on the ecology and biology of polychaete chemoreception, particularly as it mediates reproduction, recruitment, and feeding, discusses the chemosensory structures of polychaetes, and describes recent advances in our understanding of chemoreception mechanisms in polychaetes.

scholarly journals Albendazole reduces hepatic inflammation and endoplasmic reticulum-stress in a mouse model of chronic Echinococcus multilocularis infection

2022 ◽  
Vol 16 (1) ◽  
pp. e0009192
Author(s):  
Michael Weingartner ◽  
Simon Stücheli ◽  
Fadi Jebbawi ◽  
Bruno Gottstein ◽  
Guido Beldi ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Endoplasmic Reticulum Stress ◽  
Echinococcus Multilocularis ◽  
Molecular Mechanisms ◽  
Disease Recurrence ◽  
Unfolded Protein ◽  
Programmed Death ◽  
Protein Response ◽  
Host Parasite ◽  
Related Proteins

Background Echinococcus multilocularis causes alveolar echinococcosis (AE), a rising zoonotic disease in the northern hemisphere. Treatment of this fatal disease is limited to chemotherapy using benzimidazoles and surgical intervention, with frequent disease recurrence in cases without radical surgery. Elucidating the molecular mechanisms underlying E. multilocularis infections and host-parasite interactions ultimately aids developing novel therapeutic options. This study explored an involvement of unfolded protein response (UPR) and endoplasmic reticulum-stress (ERS) during E. multilocularis infection in mice. Methods E. multilocularis- and mock-infected C57BL/6 mice were subdivided into vehicle, albendazole (ABZ) and anti-programmed death ligand 1 (αPD-L1) treated groups. To mimic a chronic infection, treatments of mice started six weeks post i.p. infection and continued for another eight weeks. Liver tissue was then collected to examine inflammatory cytokines and the expression of UPR- and ERS-related genes. Results E. multilocularis infection led to an upregulation of UPR- and ERS-related proteins in the liver, including ATF6, CHOP, GRP78, ERp72, H6PD and calreticulin, whilst PERK and its target eIF2α were not affected, and IRE1α and ATF4 were downregulated. ABZ treatment in E. multilocularis infected mice reversed, or at least tended to reverse, these protein expression changes to levels seen in mock-infected mice. Furthermore, ABZ treatment reversed the elevated levels of interleukin (IL)-1β, IL-6, tumor necrosis factor (TNF)-α and interferon (IFN)-γ in the liver of infected mice. Similar to ABZ, αPD-L1 immune-treatment tended to reverse the increased CHOP and decreased ATF4 and IRE1α expression levels. Conclusions and significance AE caused chronic inflammation, UPR activation and ERS in mice. The E. multilocularis-induced inflammation and consecutive ERS was ameliorated by ABZ and αPD-L1 treatment, indicating their effectiveness to inhibit parasite proliferation and downregulate its activity status. Neither ABZ nor αPD-L1 themselves affected UPR in control mice. Further research is needed to elucidate the link between inflammation, UPR and ERS, and if these pathways offer potential for improved therapies of patients with AE.

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