Individuality in the Immune Repertoire and Induced Response of the Sponge Halichondria panicea

The animal immune system mediates host-microbe interactions from the host perspective. Pattern recognition receptors (PRRs) and the downstream signaling cascades they induce are a central part of animal innate immunity. These molecular immune mechanisms are still not fully understood, particularly in terms of baseline immunity vs induced specific responses regulated upon microbial signals. Early-divergent phyla like sponges (Porifera) can help to identify the evolutionarily conserved mechanisms of immune signaling. We characterized both the expressed immune gene repertoire and the induced response to lipopolysaccharides (LPS) in Halichondria panicea, a promising model for sponge symbioses. We exposed sponges under controlled experimental conditions to bacterial LPS and performed RNA-seq on samples taken 1h and 6h after exposure. H. panicea possesses a diverse array of putative PRRs. While part of those PRRs was constitutively expressed in all analyzed sponges, the majority was expressed individual-specific and regardless of LPS treatment or timepoint. The induced immune response by LPS involved differential regulation of genes related to signaling and recognition, more specifically GTPases and post-translational regulation mechanisms like ubiquitination and phosphorylation. We have discovered individuality in both the immune receptor repertoire and the response to LPS, which may translate into holobiont fitness and susceptibility to stress. The three different layers of immune gene control observed in this study, - namely constitutive expression, individual-specific expression, and induced genes -, draw a complex picture of the innate immune gene regulation in H. panicea. Most likely this reflects synergistic interactions among the different components of immunity in their role to control and respond to a stable microbiome, seawater bacteria, and potential pathogens.

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Promoter-specific regulation of PPARGC1A gene expression in human skeletal muscle

Journal of Molecular Endocrinology ◽

10.1530/jme-15-0150 ◽

2015 ◽

Vol 55 (2) ◽

pp. 159-168 ◽

Cited By ~ 12

Author(s):

Daniil V Popov ◽

Evgeny A Lysenko ◽

Tatiana F Vepkhvadze ◽

Nadia S Kurochkina ◽

Pavel A Maknovskii ◽

...

Keyword(s):

Gene Expression ◽

Skeletal Muscle ◽

Human Skeletal Muscle ◽

Stop Codon ◽

Constitutive Expression ◽

Alternative Promoter ◽

Specific Expression ◽

Post Exercise ◽

Specific Regulation ◽

Intensity Of Exercise

The goal of this study was to identify unknown transcription start sites of thePPARGC1A(PGC-1α) gene in human skeletal muscle and investigate the promoter-specific regulation ofPGC-1αgene expression in human skeletal muscle. Ten amateur endurance-trained athletes performed high- and low-intensity exercise sessions (70 min, 70% or 50%o2max). High-throughput RNA sequencing and exon–exon junction mapping were applied to analyse muscle samples obtained at rest and after exercise.PGC-1αpromoter-specific expression and activation of regulators of PGC-1α gene expression (AMPK, p38 MAPK, CaMKII, PKA and CREB1) after exercise were evaluated using qPCR and western blot. Our study has demonstrated that during post-exercise recovery, human skeletal muscle expresses thePGC-1αgene via two promoters only. As previously described, the additional exon 7a that contains a stop codon was found in all samples. Importantly, only minor levels of other splice site variants were found (and not in all samples). Constitutive expressionPGC-1αgene occurs via the canonical promoter, independent of exercise intensity and exercise-induced increase of AMPKThr172phosphorylation level. Expression ofPGC-1αgene via the alternative promoter is increased of two orders after exercise. This post-exercise expression is highly dependent on the intensity of exercise. There is an apparent association between expression via the alternative promoter and activation of CREB1.

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Intraspecific variation in immune gene expression and heritable symbiont density

PLoS Pathogens ◽

10.1371/journal.ppat.1009552 ◽

2021 ◽

Vol 17 (4) ◽

pp. e1009552

Author(s):

Holly L. Nichols ◽

Elliott B. Goldstein ◽

Omid Saleh Ziabari ◽

Benjamin J. Parker

Keyword(s):

Gene Expression ◽

Acyrthosiphon Pisum ◽

Aphid Species ◽

F1 Hybrids ◽

Immune Gene ◽

Immune Genes ◽

Immune Mechanisms ◽

Immune Gene Expression ◽

Host Microbe Interactions ◽

And Function

Host genetic variation plays an important role in the structure and function of heritable microbial communities. Recent studies have shown that insects use immune mechanisms to regulate heritable symbionts. Here we test the hypothesis that variation in symbiont density among hosts is linked to intraspecific differences in the immune response to harboring symbionts. We show that pea aphids (Acyrthosiphon pisum) harboring the bacterial endosymbiontRegiella insecticola(but not all other species of symbionts) downregulate expression of key immune genes. We then functionally link immune expression with symbiont density using RNAi. The pea aphid species complex is comprised of multiple reproductively-isolated host plant-adapted populations. These ‘biotypes’ have distinct patterns of symbiont infections: for example, aphids from theTrifoliumbiotype are strongly associated withRegiella. Using RNAseq, we compare patterns of gene expression in response toRegiellain aphid genotypes from multiple biotypes, and we show thatTrifoliumaphids experience no downregulation of immune gene expression while hostingRegiellaand harbor symbionts at lower densities. Using F1 hybrids between two biotypes, we find that symbiont density and immune gene expression are both intermediate in hybrids. We propose that in this system,Regiellasymbionts are suppressing aphid immune mechanisms to increase their density, but that some hosts have adapted to prevent immune suppression in order to control symbiont numbers. This work therefore suggests that antagonistic coevolution can play a role in host-microbe interactions even when symbionts are transmitted vertically and provide a clear benefit to their hosts. The specific immune mechanisms that we find are downregulated in the presence ofRegiellahave been previously shown to combat pathogens in aphids, and thus this work also highlights the immune system’s complex dual role in interacting with both beneficial and harmful microbes.

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Antibiotic treatment of the breadcrumb sponge Halichondria panicea and subsequent recolonization v1

10.17504/protocols.io.by7hpzj6 ◽

2021 ◽

Author(s):

Lara Schmittmann ◽

Ute U Hentschel

Keyword(s):

Antibiotic Treatment ◽

Recovery Phase ◽

Phase 3 ◽

Experimental Conditions ◽

Host Environment ◽

Halichondria Panicea ◽

Set Up ◽

Bacterial Recolonization ◽

Sponge Halichondria Panicea

This protocol generates sponges (Halichondria panicea) with a disturbed microbiome under controlled experimental conditions, in order to study bacterial recolonization dynamics. Bacteria-bacteria interactions can be analysed with this set-up within the host environment aiming at a better understanding of sponge-microbe symbiosis in vivo. It is divided into the sections 1) preparation, 2) antibiotic treatment and recovery phase, 3) recolonization with the natural microbiome and 4) sampling.

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Identification and Molecular Characterization of Geranyl Diphosphate Synthase (GPPS) Genes in Wintersweet Flower

Plants ◽

10.3390/plants9050666 ◽

2020 ◽

Vol 9 (5) ◽

pp. 666

Author(s):

Hafiz Muhammad Kamran ◽

Syed Bilal Hussain ◽

Shang Junzhong ◽

Lin Xiang ◽

Long-Qing Chen

Keyword(s):

Floral Scent ◽

Sequence Similarity ◽

Constitutive Expression ◽

Transcript Level ◽

Open Flower ◽

Specific Expression ◽

Geranyl Diphosphate ◽

Geranyl Diphosphate Synthase ◽

Transcriptome Database ◽

Flower Stage

Geranyl diphosphate synthase (GPPS) is a plastid localized enzyme that catalyzes the biosynthesis of Geranyl diphosphate (GPP), which is a universal precursor of monoterpenes. Wintersweet (Chimonanthus praecox L.), a famous deciduous flowering shrub with a strong floral scent character, could have GPPS-like homologs that are involved in monoterpenes biosynthesis, but it remains unclear. In the present study, five full-length GPPS and geranylgeranyl diphosphate synthases (GGPPS) genes were identified in the wintersweet transcriptome database. The isolated cDNAs showed high protein sequence similarity with the other plants GPPS and GGPPS. The phylogenetic analysis further classified these cDNAs into four distinct clades, representing heterodimeric GPPS small subunits (SSU1 and SSU2), homodimeric GPPS, and GGPPS. Analysis of temporal expression revealed that all genes have the highest transcript level at the full-open flower stage. From tissue-specific expression analysis, CpGPPS.SSU1 and CpGGPPS1 were predominantly expressed in petal and flower, whereas CpGPPS.SSU2, GPPS, and GGPPS2 showed a constitutive expression. Additionally, the subcellular localization assay identified the chloroplast localization of SSUs and GGPPSs proteins, and the yeast two-hybrid assay showed that both CpGPPS.SSU1 and CpGPPS.SSU2 can interact with the GGPPS proteins. Taken together, these preliminary results suggest that the heterodimeric GPPS can regulate floral scent biosynthesis in wintersweet flower.

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Evolution and Expression of the Immune System of a Facultatively Anadromous Salmonid

Frontiers in Immunology ◽

10.3389/fimmu.2021.568729 ◽

2021 ◽

Vol 12 ◽

Author(s):

Thomas J. Colgan ◽

Peter A. Moran ◽

Louise C. Archer ◽

Robert Wynne ◽

Stephen A. Hutton ◽

...

Keyword(s):

Life Cycle ◽

Immune System ◽

Brown Trout ◽

Salmo Trutta ◽

Whole Genome Duplication ◽

Genome Duplication ◽

Immune Gene ◽

Whole Genome ◽

Gene Repertoire ◽

Immune Genes

Vertebrates have evolved a complex immune system required for the identification of and coordinated response to harmful pathogens. Migratory species spend periods of their life-cycle in more than one environment, and their immune system consequently faces a greater diversity of pathogens residing in different environments. In facultatively anadromous salmonids, individuals may spend parts of their life-cycle in freshwater and marine environments. For species such as the brown trout Salmo trutta, sexes differ in their life-histories with females more likely to migrate to sea while males are more likely to stay and complete their life-cycle in their natal river. Salmonids have also undergone a lineage-specific whole genome duplication event, which may provide novel immune innovations but our current understanding of the differences in salmonid immune expression between the sexes is limited. We characterized the brown trout immune gene repertoire, identifying a number of canonical immune genes in non-salmonid teleosts to be duplicated in S. trutta, with genes involved in innate and adaptive immunity. Through genome-wide transcriptional profiling (“RNA-seq”) of male and female livers to investigate sex differences in gene expression amplitude and alternative splicing, we identified immune genes as being generally male-biased in expression. Our study provides important insights into the evolutionary consequences of whole genome duplication events on the salmonid immune gene repertoire and how the sexes differ in constitutive immune expression.

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The Evolution and Biocatalysis of FAD2 Indicate Its Correlation to the Content of Seed Oil in Plants

International Journal of Molecular Sciences ◽

10.3390/ijms20040849 ◽

2019 ◽

Vol 20 (4) ◽

pp. 849 ◽

Cited By ~ 1

Author(s):

Man Zhao ◽

Wenyi Wang ◽

Lei Wei ◽

Peng Chen ◽

Li Peng ◽

...

Keyword(s):

Oil Content ◽

Unsaturated Fatty Acids ◽

Fatty Acid Desaturase ◽

Constitutive Expression ◽

Strongly Correlated ◽

Specific Expression ◽

Directed Mutation ◽

History Of ◽

Main Components ◽

Total Oil

Unsaturated fatty acids are the main components of vegetable oils. Fatty acid desaturase 2 (FAD2) catalyzes oleic acid (OA) into linoleic acid (LA) transformations, which are essential to the profile of FAs in seeds. To further understand the roles of FAD2s in the synthesis of oil, the evolution and biocatalysis of FAD2s were comprehensively analyzed. The evolution history of the FAD2 gene family showed that most of the FAD2 genes formed monophyletic clades except in eudicots. The FAD2 genes in some eudicots diverged into constitutive and seed-specific expression clades. Notably, the biocatalysis of seed-specific or -abundant expression FAD2s in soybean, perilla, rice, and spruce revealed that their catalytic activity was strongly correlated with the total oil content of their seeds in nature. Additionally, it was found that I and Y in site 143 of GmaFAD2-1 were strictly conserved in the seed-specific and constitutive expression clades of Fabaceae, respectively. Furthermore, the site-directed mutation demonstrated that I and Y are vital to improving and reducing the activity of GmaFAD2s. Therefore, the results indicate that the activity of FAD2s in seeds might be a reference to the total oil content of seeds, and site 143 might have been specifically evolved to be required for the activity of FAD2s in some expression-diverged eudicots, especially in legumes.

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Post-transcriptional and post-translational regulation of Bcl2

Biochemical Society Transactions ◽

10.1042/bst0381571 ◽

2010 ◽

Vol 38 (6) ◽

pp. 1571-1575 ◽

Cited By ~ 48

Author(s):

Shaun Willimott ◽

Simon D. Wagner

Keyword(s):

Translational Regulation ◽

Transcriptional Control ◽

Rna Binding ◽

Constitutive Expression ◽

Regulatory Elements ◽

Therapeutic Approaches ◽

Internal Ribosome Entry ◽

Essential Function ◽

Cellular Stresses ◽

Bcl2 Expression

Bcl2 is an important pro-survival protein that has an essential function in normal immunity and whose constitutive expression leads to the development of lymphomas. Although transcriptional control of Bcl2 has been reported, increasing evidence suggests an important component of Bcl2 regulation is post-transcriptional. Phosphorylation of Bcl2 has been shown to enhance activity to allow response to extracellular growth-factor-mediated signals. Bcl2 mRNA contains regulatory elements in both its 5′- and 3′-UTRs (untranslated regions). An IRES (internal ribosome entry sequence) in the 5′-UTR permits continued translation in the presence of cellular stresses that reduce cap-dependent translation. The 3′-UTR of Bcl2 mRNA is 5.2 kb in length and contains multiple predicted miRNA (microRNA) and RNA-BP (RNA-binding protein)-binding sites. miR-15a and miR-16-1 have been found to inhibit Bcl2 expression in B-cells, whereas the RNA-BP nucleolin has been shown to increase Bcl2 expression by binding to the 3′-UTR and enhancing mRNA stability. Both decreased expression of miR-15a and miR-16-1 and increased nucleolin have been shown to be associated with increased Bcl2 expression and resistance to apoptosis in the common human disease, chronic lymphocytic leukaemia. miRNA-based therapeutic approaches to treat cancer are emerging. Bcl2 is highly regulated by miRNAs and is therefore an excellent candidate for such approaches.

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The c-fos cyclic AMP-responsive element conveys constitutive expression to a tissue-specific promoter

Molecular and Cellular Biology ◽

10.1128/mcb.10.5.2402-2406.1990 ◽

1990 ◽

Vol 10 (5) ◽

pp. 2402-2406

Author(s):

K A Webster ◽

L Kedes

Keyword(s):

Cyclic Amp ◽

Alternative Pathway ◽

Constitutive Expression ◽

Regulatory Elements ◽

Transcriptional Responses ◽

Specific Expression ◽

Tissue Specific ◽

Actin Promoter ◽

The Individual ◽

Alpha Actin

The c-fos and cardiac alpha-actin promoters share homologous 5' protein binding elements that are essential for serum-inducible and tissue-specific expression, respectively. Additional elements, auxiliary proteins or factor modifications, must distinguish the individual transcriptional responses of these two promoters. An element in the c-fos basal promoter that is normally responsible for transient stimulation of the fos gene in response to Ca2+ or cyclic AMP (CRE) may be able to modulate the expression of the upstream elements. We report here that this element, when inserted into the cardiac alpha-actin promoter, conveys constitutive expression to this otherwise highly restricted promoter. Additional data support the proposal that the CRE binding protein creates an alternative pathway whereby upstream regulatory elements in the cardiac alpha-actin promoter can activate transcription in a manner which circumvents the requirement for a tissue-specific environment.

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Natural and synthetic DNA elements with the CArG motif differ in expression and protein-binding properties

Molecular and Cellular Biology ◽

10.1128/mcb.11.12.6296-6305.1991 ◽

1991 ◽

Vol 11 (12) ◽

pp. 6296-6305

Author(s):

I M Santoro ◽

K Walsh

Keyword(s):

Constitutive Expression ◽

Regulatory Elements ◽

Binding Properties ◽

Specific Expression ◽

Tissue Specific ◽

Left Half ◽

Tissue Specific Expression ◽

Dna Elements ◽

The Right ◽

Natural And Synthetic

DNA elements with the CC(A/T)6GG, or CArG, motif occur in promoters that are under different regulatory controls. CArG elements from the skeletal actin, c-fos, and myogenin genes were tested for their abilities to confer tissue-specific expression on reporter genes when the individual elements were situated immediately upstream from a TATA element. The c-fos CArG element, also referred to as the serum response element (SRE), conferred basal, constitutive expression on the test promoter. The CArG motif from the myogenin gene was inactive. The skeletal actin CArG motif functioned as a muscle regulatory element (MRE) in that basal expression was detected only in muscle cultures. Muscle-specific expression from the 28-bp MRE and the 2.3-kb skeletal actin promoter was trans repressed by the Fos and Jun proteins. The expression and factor-binding properties of a series of synthetic CArG elements were analyzed. Muscle-specific expression was conferred by perfect 28-bp palindromes on the left and right halves of the skeletal actin MRE. Chimeric elements of the skeletal actin MRE and the c-fos SRE differed in their expression properties. Muscle-specific expression was observed when the left half of the MRE was fused to the right half of the SRE. Constitutive expression was conferred by a chimera with the right half of the MRE fused to the left half of the SRE and by chimeras which exchanged the central CC(A/T)6GG sequences. At least three distinct proteins specifically bound to these CArG elements. The natural and synthetic CArG elements differed in their affinities for these proteins; however, muscle-specific expression could not be attributed to differences in the binding of a single protein. Furthermore, the MRE did not bind MyoD or the myogenin-E12 heterodimer, indicating that muscle-specific expression from this element does not involve a direct interaction with these helix-loop-helix proteins. These data demonstrate that the conserved CArG motifs form the core of a family of functionally different DNA regulatory elements that may contribute to the tissue-specific expression properties of their cognate promoters.

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Clonality Analysis as a Tool To Study the Immunologic Reconstitution with Leukemia Patients Following Allogeneic Hematopoietic Stem Cell Transplantation.

Blood ◽

10.1182/blood.v104.11.5020.5020 ◽

2004 ◽

Vol 104 (11) ◽

pp. 5020-5020

Author(s):

Xin Du ◽

Yangqiu Li ◽

Jianyu Weng ◽

Zesheng Lu ◽

Rong Xie ◽

...

Keyword(s):

T Cells ◽

Stem Cell ◽

T Cell ◽

Stem Cell Transplantation ◽

Cell Transplantation ◽

T Cell Receptor ◽

Cell Receptor ◽

Gene Repertoire ◽

Hematopoietic Stem ◽

Receptor Repertoire

Abstract Introduction The extensive diversity of the mature T-cell receptor(TCR) is determined primarily by the complementarity-determining regions (CDR3) of the TCR. The CDR3 of both TCRα and TCRβ genes is generated by extensive rearrangement and fusion between the V,D,and J segments and by random insertion and deletion of junctional nucleotides, which yields final products that are quite heterogeneous in size. As a result of these gene rearrangements, each T cell has a unique TCR and the diversity of the T-cell repertoire at any specific time can be characterized by the examination of CDR3 within that population. Using CDR3 spectratying technique, normal individuals demonstrate a highly diverse and polyclonal The aim of our study was to evaluate to investigate restricted expansion of TCR Vβ gene repertoire and the reconstitution of T cell receptor repertoire following allogeneic hematopoietic stem cell transplantation. Methods Patients Ten patients(9 males, 1 females; median age 31 years,range18–45) with 6 chronic myeloid leukemia-chronic phase and 4 cases of acute myelogenous lenkemia(CR1) who underwent HLA-matching sibling or unrelated BMT and/or peripheral blood stem cell transplantation (PBSCT) at our department between July 1999 and May 2000 were considered evaluable restricted expansion of TCR Vβ gene repertoire, the reconstitution of T cell receptor repertoire and oligoclonal T Cell Expansion in Chronic Graft-Versus-Host Disease. RT-PCR and Genes scan analysis (CDR 3 length analysis). Results Only 2-18Vβ genes were found in samples from these ten patients within one year, and there are different distribution in different patients. TCR repertoire complexity was abnormal in all patients, parts of the genes were expansion and part of them were suppressed. Samples from 9 patients with GVHD show V β3 in 7 cases, V β 8 and V β 23 in 6 patients. The results of genescan show that the PCR production of peripheral blood samples from these patients disply oligoclonal. Only 5–22Vβ subfamily T cells were found in samples from these patients whose transplantation more than one year. TCR repertoire complexity was abnormal in all patients. Discussion Following allogeneic BMT, regeneration of T-cell populations with a diverse repertoire can occure by at least two mechanisms: One mechanism is a thymic-dependent pathway, which presumably involves both negative and positive selection and recapitulates fetal ontogeny. Alternatively, regeneration of peripheral T cells may occur through thymic-independent mechanisms. All patients had marked abnormalities in their spectratypes, only 5-22Vβ subfamily T cells were found in samples from these patients, most of it was influenced after transplant, although the number of circulating CD3+ T lymphocytes in these patients have restored at normal lever by flow cytometic analysis, but the CD4+ T cell subset returned slowly in these patients resulting in an inversion of the normal CD4/CD8 ratio for more than 1 year after tuansplantation. Therefore, the analysis of TCRVβ subfamily is a usuaful methods and techniques for monitoring immune reconstitution after transplant.

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