Influence of habitat change from land to sea on the evolution of antimicrobial peptide gene families, including β‐defensin gene clusters, in mammals

AbstractThere is increasing evidence that some functionally related, co-expressed genes cluster within eukaryotic genomes. We present a novel pipeline that delineates such eukaryotic gene clusters. Using this tool for bread wheat, we uncovered 44 clusters of genes that are responsive to the fungal pathogen Fusarium graminearum. As expected, these Fusarium-responsive gene clusters (FRGCs) included metabolic gene clusters, many of which are associated with disease resistance, but hitherto not described for wheat. However, the majority of the FRGCs are non-metabolic, many of which contain clusters of paralogues, including those implicated in plant disease responses, such as glutathione transferases, MAP kinases, and germin-like proteins. 20 of the FRGCs encode nonhomologous, non-metabolic genes (including defence-related genes). One of these clusters includes the characterised Fusarium resistance orphan gene, TaFROG. Eight of the FRGCs map within 6 FHB resistance loci. One small QTL on chromosome 7D (4.7 Mb) encodes eight Fusarium-responsive genes, five of which are within a FRGC. This study provides a new tool to identify genomic regions enriched in genes responsive to specific traits of interest and applied herein it highlighted gene families, genetic loci and biological pathways of importance in the response of wheat to disease.

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Genomic Characteristics and Comparative Genomics Analysis of Two Chinese Corynespora cassiicola Strains Causing Corynespora Leaf Fall (CLF) Disease

Journal of Fungi ◽

10.3390/jof7060485 ◽

2021 ◽

Vol 7 (6) ◽

pp. 485

Author(s):

Boxun Li ◽

Yang Yang ◽

Jimiao Cai ◽

Xianbao Liu ◽

Tao Shi ◽

...

Keyword(s):

Comparative Genomics ◽

Single Molecule ◽

Rubber Tree ◽

Gene Families ◽

Gene Clusters ◽

The Philippines ◽

Tree Plantations ◽

Comparative Genomic ◽

Corynespora Cassiicola ◽

Leaf Fall

Rubber tree Corynespora leaf fall (CLF) disease, caused by the fungus Corynespora cassiicola, is one of the most damaging diseases in rubber tree plantations in Asia and Africa, and this disease also threatens rubber nurseries and young rubber plantations in China. C. cassiicola isolates display high genetic diversity, and virulence profiles vary significantly depending on cultivar. Although one phytotoxin (cassicolin) has been identified, it cannot fully explain the diversity in pathogenicity between C. cassiicola species, and some virulent C. cassiicola strains do not contain the cassiicolin gene. In the present study, we report high-quality gapless genome sequences, obtained using short-read sequencing and single-molecule long-read sequencing, of two Chinese C. cassiicola virulent strains. Comparative genomics of gene families in these two stains and a virulent CPP strain from the Philippines showed that all three strains experienced different selective pressures, and metabolism-related gene families vary between the strains. Secreted protein analysis indicated that the quantities of secreted cell wall-degrading enzymes were correlated with pathogenesis, and the most aggressive CCP strain (cassiicolin toxin type 1) encoded 27.34% and 39.74% more secreted carbohydrate-active enzymes (CAZymes) than Chinese strains YN49 and CC01, respectively, both of which can only infect rubber tree saplings. The results of antiSMASH analysis showed that all three strains encode ~60 secondary metabolite biosynthesis gene clusters (SM BGCs). Phylogenomic and domain structure analyses of core synthesis genes, together with synteny analysis of polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) gene clusters, revealed diversity in the distribution of SM BGCs between strains, as well as SM polymorphisms, which may play an important role in pathogenic progress. The results expand our understanding of the C. cassiicola genome. Further comparative genomic analysis indicates that secreted CAZymes and SMs may influence pathogenicity in rubber tree plantations. The findings facilitate future exploration of the molecular pathogenic mechanism of C. cassiicola.

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Paneth cells of the human small intestine express an antimicrobial peptide gene

Journal of Biological Chemistry ◽

10.1016/s0021-9258(18)50079-x ◽

1992 ◽

Vol 267 (32) ◽

pp. 23216-23225

Author(s):

D.E. Jones ◽

C.L. Bevins

Keyword(s):

Small Intestine ◽

Antimicrobial Peptide ◽

Paneth Cells ◽

Human Small Intestine ◽

Peptide Gene

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Identification of multiple male reproductive tract-specific proteins that regulate sperm migration through the oviduct in mice

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1908736116 ◽

2019 ◽

Vol 116 (37) ◽

pp. 18498-18506 ◽

Cited By ~ 13

Author(s):

Yoshitaka Fujihara ◽

Taichi Noda ◽

Kiyonori Kobayashi ◽

Asami Oji ◽

Sumire Kobayashi ◽

...

Keyword(s):

Membrane Protein ◽

Male Fertility ◽

Reproductive Tract ◽

Gene Families ◽

Gene Clusters ◽

Mutant Mice ◽

Male Reproductive Tract ◽

Sperm Migration ◽

Specific Proteins ◽

Multiple Male

CRISPR/Cas9-mediated genome editing technology enables researchers to efficiently generate and analyze genetically modified animals. We have taken advantage of this game-changing technology to uncover essential factors for fertility. In this study, we generated knockouts (KOs) of multiple male reproductive organ-specific genes and performed phenotypic screening of these null mutant mice to attempt to identify proteins essential for male fertility. We focused on making large deletions (dels) within 2 gene clusters encoding cystatin (CST) and prostate and testis expressed (PATE) proteins and individual gene mutations in 2 other gene families encoding glycerophosphodiester phosphodiesterase domain (GDPD) containing and lymphocyte antigen 6 (Ly6)/Plaur domain (LYPD) containing proteins. These gene families were chosen because many of the genes demonstrate male reproductive tract-specific expression. AlthoughGdpd1andGdpd4mutant mice were fertile, disruptions ofCstandPategene clusters andLypd4resulted in male sterility or severe fertility defects secondary to impaired sperm migration through the oviduct. While absence of the epididymal protein families CST and PATE affect the localization of the sperm membrane protein A disintegrin and metallopeptidase domain 3 (ADAM3), the sperm acrosomal membrane protein LYPD4 regulates sperm fertilizing ability via an ADAM3-independent pathway. Thus, use of CRISPR/Cas9 technologies has allowed us to quickly rule in and rule out proteins required for male fertility and expand our list of male-specific proteins that function in sperm migration through the oviduct.

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Lilium Regale Wilson WRKY3 Modulates an Antimicrobial Peptide Gene, Lrdef1, During Response to Fusarium Oxysporum

10.21203/rs.3.rs-871518/v1 ◽

2021 ◽

Author(s):

Zie Wang ◽

Jie Deng ◽

Tingting Liang ◽

Linlin Su ◽

Lilei Zheng ◽

...

Keyword(s):

Antimicrobial Peptide ◽

Fusarium Oxysporum ◽

Transgenic Tobacco ◽

Sequencing Analysis ◽

Lilium Regale ◽

Expression Activity ◽

Metabolite Synthesis ◽

Lilium Regale Wilson ◽

Peptide Gene ◽

Higher Sensitivity

Abstract Background: WRKY transcription factors (TFs) play vital roles in plant growth and development, secondary metabolite synthesis, and response to biotic and abiotic stresses. In a previous transcriptome sequencing analysis of Lilium regale Wilson, we identified multiple WRKY TFs that respond to exogenous methyl jasmonate treatment and lily Fusarium wilt (Fusarium oxysporum).Results: In the present study, the WRKY TF LrWRKY3 was further analyzed to reveal its function in defense response to F. oxysporum. The LrWRKY3 protein was localized in the plant cell nucleus, and LrWRKY3 transgenic tobacco lines showed higher resistance to F. oxysporum compared with wild-type (WT) tobacco. In addition, some genes related to jasmonic acid (JA) biosynthesis, salicylic acid (SA) signal transduction, and disease resistance had higher transcriptional levels in the LrWRKY3 transgenic tobacco lines than in the WT. On the contrary, L. regale scales transiently expressing LrWRKY3 RNA interference fragments showed higher sensitivity to F. oxysporum infection. Moreover, a F. oxysporum-induced defensin gene, Def1, was isolated from L. regale, and the recombinant protein LrDef1 isolated and purified from Escherichia coli possessed antifungal activity to several phytopathogens, including F. oxysporum. Furthermore, co-expression of LrWRKY3 and the LrDef1 promoter in tobacco evidently up-regulated the expression activity of the LrDef1 promoter.Conclusions: These results clearly indicate that LrWRKY3 is an important positive regulator in response to F. oxysporum infection, and one of its targets is the antimicrobial peptide gene LrDef1.

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Giant African snail genomes provide insights into molluscan whole-genome duplication and aquatic-terrestrial transition

10.1101/2020.02.02.930693 ◽

2020 ◽

Cited By ~ 2

Author(s):

Conghui Liu ◽

Yuwei Ren ◽

Zaiyuan Li ◽

Qi Hu ◽

Lijuan Yin ◽

...

Keyword(s):

Whole Genome Duplication ◽

Genome Duplication ◽

Terrestrial Ecosystems ◽

Gene Families ◽

Gene Clusters ◽

Immune Defense ◽

Whole Genome ◽

Genomic Plasticity ◽

Ecological Adaptability ◽

Chromosome Level

AbstractWhole-genome duplication (WGD) has been observed across a wide variety of eukaryotic groups, contributing to evolutionary diversity and environmental adaptability. Mollusks are the second largest group of animals, and are among the organisms that have successfully adapted to the nonmarine realm through aquatic-terrestrial (A-T) transition, and no comprehensive research on WGD has been reported in this group. To explore WGD and the A-T transition in Mollusca, we assembled a chromosome-level reference genome for the giant African snail Achatina immaculata, a global invasive species, and compared the genomes of two giant African snails (A. immaculata and Achatina fulica) to the other available mollusk genomes. The chromosome-level macrosynteny, colinearity blocks, Ks peak and Hox gene clusters collectively suggested the occurrence of a WGD event shared by A. immaculata and A. fulica. The estimated timing of this WGD event (∼70 MYA) was close to the speciation age of the Sigmurethra-Orthurethra (within Stylommatophora) lineage and the Cretaceous-Tertiary (K-T) mass extinction, indicating that the WGD reported herein may have been a common event shared by all Sigmurethra-Orthurethra species and could have conferred ecological adaptability and genomic plasticity allowing the survival of the K-T extinction. Based on macrosynteny, we deduced an ancestral karyotype containing 8 conserved clusters for the Gastropoda-Bivalvia lineage. To reveal the mechanism of WGD in shaping adaptability to terrestrial ecosystems, we investigated gene families related to the respiration, aestivation and immune defense of giant African snails. Several mucus-related gene families expanded early in the Stylommatophora lineage, functioning in water retention, immune defense and wound healing. The hemocyanins, PCK and FBP families were doubled and retained after WGD, enhancing the capacity for gas exchange and glucose homeostasis in aestivation. After the WGD, zinc metalloproteinase genes were highly tandemly duplicated to protect tissue against ROS damage. This evidence collectively suggests that although the WGD may not have been the direct driver of the A-T transition, it provided an important legacy for the terrestrial adaptation of the giant African snail.

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Functional Characterization of a Novel Promoter Element Required for an Innate Immune Response in Drosophila

Molecular and Cellular Biology ◽

10.1128/mcb.23.22.8272-8281.2003 ◽

2003 ◽

Vol 23 (22) ◽

pp. 8272-8281 ◽

Cited By ~ 21

Author(s):

Hanna Uvell ◽

Ylva Engström

Keyword(s):

Gene Expression ◽

Antimicrobial Peptide ◽

Functional Characterization ◽

Binding Activity ◽

Innate Immune ◽

Site Directed Mutagenesis ◽

Promoter Element ◽

Peptide Gene ◽

Inducible Genes

ABSTRACT Innate immune reactions are crucial processes of metazoans to protect the organism against overgrowth of faster replicating microorganisms. Drosophila melanogaster is a precious model for genetic and molecular studies of the innate immune system. In response to infection, the concerted action of a battery of antimicrobial peptides ensures efficient killing of the microbes. The induced gene expression relies on translocation of the Drosophila Rel transcription factors Relish, Dif, and Dorsal to the nucleus where they bind to κB-like motifs in the promoters of the inducible genes. We have identified another putative promoter element, called region 1 (R1), in a number of antimicrobial peptide genes. Site-directed mutagenesis of the R1 site diminished Cecropin A1 (CecA1) expression in transgenic Drosophila larvae and flies. Infection of flies induced a nuclear R1-binding activity that was unrelated to the κB-binding activity in the same extracts. Although the R1 motif was required for Rel protein-mediated CecA1 expression in cotransfection experiments, our data argue against it being a direct target for the Drosophila Rel proteins. We propose that the R1 and κB motifs are targets for distinct regulatory complexes that act in concert to promote high levels of antimicrobial peptide gene expression in response to infection.

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