Transposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable elements in the expansion of nucleotide-binding and ...leucine-rich-repeat proteins (NLRs), the major disease-resistance gene families, has been unexplored in plants.
We report two high-quality de novo genomes (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum) for peppers. Dynamic genome rearrangements involving translocations among chromosomes 3, 5, and 9 were detected in comparison between C. baccatum and the two other peppers. The amplification of athila LTR-retrotransposons, members of the gypsy superfamily, led to genome expansion in C. baccatum. In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs are abundant across the angiosperms and, in most cases, are lineage-specific.
Our study reveals that retroduplication has played key roles for the massive emergence of NLR genes including functional disease-resistance genes in pepper plants.
Periodontitis is a common disease characterized by chronic inflammation and tissue destruction of gums. Human periodontal ligament stem cells (PDLSCs), derived from the periodontium, have stem cell ...properties similar to those of mesenchymal stem cells. PDLSCs possess not only the potential to differentiate into other tissues, but also immunomodulatory abilities. Macrophages play a critical role in periodontal disease, but little is known regarding the role of PDLSCs in macrophage modulation during inflammation. In this study, we investigated the effect of PDLSCs on the macrophage cell line. While the conditioned media from PDLSCs under normal culture conditions did not affect macrophage polarization, the lipopolysaccharide (LPS)-preconditioned PDLSCs induced significant changes in M1 polarization. Extracellular vesicles (EVs) isolated from the conditioned media of LPS-preconditioned PDLSCs induced strong M1 polarization of macrophages. Additionally, the M1 polarization was abolished by DNase I treatment of EVs. Therefore, the LPS-stimulated PDLSCs induce M1 polarization of macrophages through EVs, suggesting that the EVs from PDLSCs might be a potential therapeutic target for inflammation in the periodontium.
Design and fabrication of a 1-MW inductive power transfer (IPT) system that supplies power to the vehicle in real time without any battery charge is proposed for a high-speed train. The IPT system ...consists of a 1-MW resonant inverter, a 128-m transmitter, four pickups, including rectifiers, and a wireless feedback network to maintain a constant output voltage of the pickups. The operating frequency of the system is 60 kHz to achieve efficient power transfer with a large air gap. The measured efficiency of the IPT system at the 818-kW output power of the pickups for the 5-cm air gap is 82.7%. The electromagnetic field and the induced voltage at the rail are also measured for safety evaluation. The fabricated IPT system was adapted to the high-speed train, and the train successfully accelerates to a speed of 10 km/h according to startup procedures.
Extracellular vesicles (EVs) contain a variety of biomolecules and provide information about the cells that produce them. EVs from cancer cells found in urine can be used as biomarkers to detect ...cancer, enabling early diagnosis and treatment. The potential of alpha-2-macroglobulin (A2M) and clusterin (CLU) as novel diagnostic urinary EV (uEV) biomarkers for bladder cancer (BC) was demonstrated previously. To validate the diagnostic value of these proteins in uEVs in a large BC cohort, urine handling conditions before uEV isolation should be optimized during sample transportation from medical centers. In this study, we analyzed the uEV protein quantity, EV particle number, and uEV-A2M/CLU after urine storage at 20°C and 4°C for 0–6 days, each. A2M and CLU levels in uEVs were relatively stable when stored at 4°C for a maximum of three days and at 20°C for up to 24 h, with minimal impact on analysis results. Interestingly, pre-processing to remove debris and cells by centrifugation and filtration of urine did not show any beneficial effects on the preservation of protein biomarkers of uEVs during storage. Here, the importance of optimizing shipping conditions to minimize the impact of pre-analytical handling on the uEVs protein biomarkers was emphasized. These findings provide insights for the development of clinical protocols that use uEVs for diagnostic purposes.
Many cytokines produced by Kaposi's sarcoma‐associated herpesvirus (KSHV)‐infected cells have been shown to participate in the pathogenesis of KSHV. Determination of the exact role of cytokines in ...Kaposi's sarcoma (KS) pathogenesis is limited, however, by the difficulty to manipulate the target genes in human endothelial cells. In this study, we sought to elucidate the role of cytokines in KSHV‐infected human immortalized endothelial cell line (HuARLT cells) by knockout (KO) of the corresponding target genes using the CRISPR/Cas9 system. The cytokine production profile of KSHV‐infected HuARLT cells was analyzed using a protein array, and several cytokines were found to be highly upregulated following KSHV infection. This study focused on CXCL1, which was investigated by knocked out in HuARLT cells. KSHV‐infected CXCL1 KO cells underwent increased cell death compared to KSHV‐infected wild‐type (WT) cells and mock‐infected CXCL1 KO cells. Lytic replication was not observed in KSHV‐infected WT nor CXCL1 KO cells. Phosphorylation of STAT3 was significantly suppressed in KSHV‐infected CXCL1 KO cells. Additionally, inhibitors of STAT3 and CXCL1 induced cell death in KSHV‐infected endothelial cells. Our results show that CXCL1 production is required for the survival of KSHV‐infected endothelial cells, and the CXCL1 to STAT3 phosphorylation signaling pathway may be a therapeutic target for KS.
• During the evolution of land plants from aquatic to terrestrial environments, their aerial surfaces were surrounded by cuticle composed of cutin and cuticular waxes to protect them from ...environmental stresses. Glycerol-3-phosphate acyltransferase (GPAT) harboring bifunctional sn-2 acyltransferase/phosphatase activity produces 2-monoacylglycerol, a precursor for cutin synthesis.
• Here, we report that bifunctional sn-2 GPATs play roles in cuticle biosynthesis and game-tophore development of Physcomitrella patens.
• Land plant-type cuticle was observed in gametophores but not in protonema. The expression of endoplasmic reticulum-localized PpGPATs was significantly upregulated in game-tophores compared with protonema. Floral organ fusion and permeable cuticle phenotypes of Arabidopsis gpat6-2 petals were rescued to the wild type (WT) by the expression of PpGPAT2 or PpGPAT4. Disruption of PpGPAT2 and PpGPAT4 caused a significant reduction of total cutin loads, and a prominent decrease in the levels of palmitic and 10,16-dihydroxydecanoic acids, which are major cutin monomers in gametophores. Δppgpat2 mutants displayed growth retardation, delayed gametophore development, increased cuticular permeability, and reduced tolerance to drought, osmotic and salt stresses compared to the WT.
• Genome-wide analysis of genes encoding acyltransferase or phosphatase domains suggested that the occurrence of sn-2 GPATs with both domains may be a key event in cuticle biogenesis of land plants.
SUMMARY
Plant nucleotide‐binding domain leucine‐rich‐repeat receptor (NLR) confers disease resistance to various pathogens by recognizing effectors derived from the pathogen. Previous studies have ...shown that overexpression of the CC domain in several NLRs triggers cell death, implying that the CC domain plays an important role as a signaling module. However, how CC domain transduces immune signals remains largely unknown. A Potyvirus‐resistant NLR protein, Pvr4, possesses a CC domain (CC
Pvr4
) that induces cell death upon transient overexpression in
Nicotiana benthamiana
. In this study, loss‐of‐function mutants were generated by error‐prone PCR‐based random mutagenesis to understand the molecular mechanisms underlying CC
Pvr4
‐mediated cell death. Cell biology and biochemical studies revealed that M16 and Q52 in the α1 and α2 helices, respectively, are crucial for protein stability, and mutation of these residues disrupts localization to the plasma membrane and oligomerization activity. The increase of the protein stability of these mutants by tagging a green fluorescent protein (GFP) variant led to restoration of cell death‐inducing activity and plasma membrane localization. Another mutant, I7E in the very N‐terminal region, lost cell death‐inducing activity by weakening the interaction with plasma membrane H
+
‐ATPase compared to CC
Pvr4
, although the protein remained in the plasma membrane. Moreover, most of the mutated residues are on the outer surface of the funnel shape in the predicted pentameric CC
Pvr4
, implying that the disordered N‐terminal region plays a crucial role in association with PMA as well as targeting to the plasma membrane. This work could provide insights into the molecular mechanisms of cell death induced by NLR immune receptors.
Significance Statement
Our work demonstrates that pepper Pvr4, a resistance protein for potyviruses, targets to the plasma membrane to trigger defense responses including hypersensitive resistance and N‐terminal coiled‐coil domain is responsible for its localization and immune responses. The mutants generated from random mutagenesis and homology‐based structure modeling revealed that of outer surface of CC domain composed of α1 and α2 helices are crucial for their protein stability, plasma membrane targeting and self‐association.
Summary
Plants possess hundreds of intracellular immune receptors encoding nucleotide‐binding domain leucine‐rich repeat (NLR) proteins. Full‐length NLRs or a specific domain of NLRs often induce ...plant cell death in the absence of pathogen infection.
In this study we used genome‐wide transient expression analysis to identify a group of NLRs (ANLs; ancient and autonomous NLRs) carrying autoactive coiled‐coil (CCA) domains in pepper (Capsicum annuum). CCA‐mediated cell death mimics hypersensitive cell death triggered by the interaction between NLRs and pathogen effectors.
Sequence alignment and mutagenesis analyses revealed that the intact α1 helix of CCAs is critical for both CCA‐ and ANL‐mediated cell death. Cell death induced by CCAs does not require NRG1/ADR1 or NRC type helper NLRs, suggesting ANLs may function as singleton NLRs. We also found that CCAs localize to the plasma membrane, as demonstrated for Arabidopsis singleton NLR ZAR1. Extended studies revealed that autoactive CCAs are well conserved in other Solanaceae plants as well as in rice, a monocot plant. Further phylogenetic analyses revealed that ANLs are present in all tested seed plants (spermatophytes).
Our study not only uncovers the autonomous NLR clade in plants but also provides powerful resources for dissecting the underlying molecular mechanism of NLR‐mediated cell death in plants.
Recently, a network-based mobility management protocol called Proxy Mobile IPv6 (PMIPv6) is being actively standardized by the IETF NETLMM working group, and is starting to attract considerable ...attention among the telecommunication and Internet communities. Unlike the various existing protocols for IP mobility management such as Mobile IPv6 (MIPv6), which are host-based approaches, a network-based approach such as PMIPv6 has salient features and is expected to expedite the real deployment of IP mobility management. In this article, starting by showing the validity of a network-based approach, we present qualitative and quantitative analyses of the representative host-based and network-based mobility management approaches (i.e., MIPv6 and PMIPv6), which highlight the main desirable features and key strengths of PMIPv6. Furthermore, a comprehensive comparison among the various existing well-known mobility support protocols is investigated. Although the development of PMIPv6 is at an early stage yet, it is strongly expected that PMIPv6 will be a promising candidate solution for realizing the next-generation all-IP mobile networks.
Key message
Genotyping data of a comprehensive Korean soybean collection obtained using a large SNP array were used to clarify global distribution patterns of soybean and address the evolutionary ...history of soybean.
Understanding diversity and evolution of a crop is an essential step to implement a strategy to expand its germplasm base for crop improvement research. Accessions intensively collected from Korea, which is a small but central region in the distribution geography of soybean, were genotyped to provide sufficient data to underpin population genetic questions. After removing natural hybrids and duplicated or redundant accessions, we obtained a non-redundant set comprising 1957 domesticated and 1079 wild accessions to perform population structure analyses. Our analysis demonstrates that while wild soybean germplasm will require additional sampling from diverse indigenous areas to expand the germplasm base, the current domesticated soybean germplasm is saturated in terms of genetic diversity. We then showed that our genome-wide polymorphism map enabled us to detect genetic loci underlying flower color, seed-coat color, and domestication syndrome. A representative soybean set consisting of 194 accessions was divided into one domesticated subpopulation and four wild subpopulations that could be traced back to their geographic collection areas. Population genomics analyses suggested that the monophyletic group of domesticated soybeans was likely originated at a Japanese region. The results were further substantiated by a phylogenetic tree constructed from domestication-associated single nucleotide polymorphisms identified in this study.
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