Peptidome: Chaos or Inevitability Lyapina, Irina; Ivanov, Vadim; Fesenko, Igor
International journal of molecular sciences,
12/2021, Letnik:
22, Številka:
23
Journal Article
Recenzirano
Odprti dostop
Thousands of naturally occurring peptides differing in their origin, abundance and possible functions have been identified in the tissue and biological fluids of vertebrates, insects, fungi, plants ...and bacteria. These peptide pools are referred to as intracellular or extracellular peptidomes, and besides a small proportion of well-characterized peptide hormones and defense peptides, are poorly characterized. However, a growing body of evidence suggests that unknown bioactive peptides are hidden in the peptidomes of different organisms. In this review, we present a comprehensive overview of the mechanisms of generation and properties of peptidomes across different organisms. Based on their origin, we propose three large peptide groups-functional protein "degradome", small open reading frame (smORF)-encoded peptides (smORFome) and specific precursor-derived peptides. The composition of peptide pools identified by mass-spectrometry analysis in human cells, plants, yeast and bacteria is compared and discussed. The functions of different peptide groups, for example the role of the "degradome" in promoting defense signaling, are also considered.
Plants have evolved a sophisticated innate immune system to cope with a diverse range of phytopathogens and insect herbivores. Plasma-membrane-localized pattern recognition receptors (PRRs), such as ...receptor-like kinases (RLK), recognize special signals, pathogen- or damage-associated molecular patterns (PAMPs or DAMPs), and trigger immune responses. A growing body of evidence shows that many peptides hidden in both plant and pathogen functional protein sequences belong to the group of such immune signals. However, the origin, evolution, and release mechanisms of peptide sequences from functional and nonfunctional protein precursors, known as cryptic peptides, are largely unknown. Various special proteases, such as metacaspase or subtilisin-like proteases, are involved in the release of such peptides upon activation during defense responses. In this review, we discuss the roles of cryptic peptide sequences hidden in the structure of functional proteins in plant defense and plant-pathogen interactions.
Genomes contain millions of short (<100 codons) open reading frames (sORFs), which are usually dismissed during gene annotation. Nevertheless, peptides encoded by such sORFs can play important ...biological roles, and their impact on cellular processes has long been underestimated. Here, we analyzed approximately 70,000 transcribed sORFs in the model plant
(moss). Several distinct classes of sORFs that differ in terms of their position on transcripts and the level of evolutionary conservation are present in the moss genome. Over 5000 sORFs were conserved in at least one of 10 plant species examined. Mass spectrometry analysis of proteomic and peptidomic data sets suggested that tens of sORFs located on distinct parts of mRNAs and long noncoding RNAs (lncRNAs) are translated, including conserved sORFs. Translational analysis of the sORFs and main ORFs at a single locus suggested the existence of genes that code for multiple proteins and peptides with tissue-specific expression. Functional analysis of four lncRNA-encoded peptides showed that sORFs-encoded peptides are involved in regulation of growth and differentiation in moss. Knocking out lncRNA-encoded peptides resulted in a decrease of moss growth. In contrast, the overexpression of these peptides resulted in a diverse range of phenotypic effects. Our results thus open new avenues for discovering novel, biologically active peptides in the plant kingdom.
In a system of dielectric matrix–conducting particles, the dielectric characteristics are analyzed over a wide frequency range (3–37 GHz). Experimental values of the dielectric constant
ε
′ and ...dielectric loss tangent tan
δ
are presented for pressureless sintered AlN-based composites with different contents of the conducting particles (Mo, W, and TiN) within the interval from 0% to the percolation threshold. Both the real
ε
′ and imaginary
ε
″ parts of the dielectric constant of the investigated composites monotonically increased, reaching maximum values (
ε
′ = 15 – 26.5,
ε
″ = 0.14–0.28) when the content of the conductive particles approached the percolation threshold. The dielectric loss tangent of the composites, depending on the conducting particle content, reached values of 0.0085 for AlN–16.6%Mo, 0.0095 for AlN–16%W, and 0.0105 for AlN–20.4%TiN. The dielectric losses
ε
″ in the AlN-based composites, as long as they remain nonconductive for the direct current, are low compared to losses of
ε
″ = 0.04 in polycrystalline AlN ceramics and exceed them by only 4–7 times. A relationship between the dielectric losses and the level of microwave absorption has been established. The dielectric characteristics, electrical resistance, and thermal conductivity of the produced AlN-based composites and their achievement of a high absorption of the microwave radiation (
L
= 23–32 dB/cm) make these materials promising bulk absorbers in microwave devices (TWTs, klystrons).
Plant-virus interactions are frequently influenced by elevated temperature, which often increases susceptibility to a virus, a scenario described for potato cultivar Chicago infected with potato ...virus Y (PVY). In contrast, other potato cultivars such as Gala may have similar resistances to PVY at both normal (22 °C) and high (28 °C) temperatures. To elucidate the mechanisms of temperature-independent antivirus resistance in potato, we analysed responses of Gala plants to PVY at different temperatures using proteomic, transcriptional and metabolic approaches. Here we show that in Gala, PVY infection generally upregulates the accumulation of major enzymes associated with the methionine cycle (MTC) independently of temperature, but that temperature (22 °C or 28 °C) may finely regulate what classes accumulate. The different sets of MTC-related enzymes that are up-regulated at 22 °C or 28 °C likely account for the significantly increased accumulation of S-adenosyl methionine (SAM), a key component of MTC which acts as a universal methyl donor in methylation reactions. In contrast to this, we found that in cultivar Chicago, SAM levels were significantly reduced which correlated with the enhanced susceptibility to PVY at high temperature. Collectively, these data suggest that MTC and its major transmethylation function determines resistance or susceptibility to PVY.
Plants utilize a plethora of peptide signals to regulate their immune response. Peptide ligands and their cognate receptors involved in immune signaling share common motifs among many species of ...vascular plants. However, the origin and evolution of immune peptides is still poorly understood. Here, we searched for genes encoding small secreted peptides in the genomes of three bryophyte lineages—mosses, liverworts and hornworts—that occupy a critical position in the study of land plant evolution. We found that bryophytes shared common predicted small secreted peptides (SSPs) with vascular plants. The number of SSPs is higher in the genomes of mosses than in both the liverwort
Marchantia polymorpha
and the hornwort
Anthoceros sp
. The synthetic peptide elicitors—AtPEP and StPEP—specific for vascular plants, triggered ROS production in the protonema of the moss
Physcomitrella patens
, suggesting the possibility of recognizing peptide ligands from angiosperms by moss receptors. Mass spectrometry analysis of the moss
Physcomitrella patens
, both the wild type and the Δ
cerk
mutant secretomes, revealed peptides that specifically responded to chitosan treatment, suggesting their role in immune signaling.
Small open reading frames (<100 codons) that are located on long noncoding RNAs (lncRNAs) can encode functional microproteins. These microproteins are shown to play important roles in different ...cellular processes, such as cell proliferation, development and disease response 1–6. However, there are only a few known lncRNA-encoded functional microproteins in plants. One such microprotein that was named PSEP3, was identified in the moss Physcomitrium patens by mass-spectrometry analysis. 57-aa PSEP3 contains Low Complexity Region (LCR) enriched with proline. We have previously shown that PSEP3 is translated in protonemata and gametophores of P. patens, and its knockout (KO line) or overexpression (OE line) affects protonemata growth 7. We performed a quantitative proteomic analysis of the mutant lines with PSEP3 knockout and overexpression. 7-days old protonemata of wild type (WT line) and both mutant lines (KO and OE) were collected and used for iTRAQ-based proteomic experiments. LC-MS/MS data were processed using PEAKS Studio v.8 software with protein identification based on a Phytozome protein database. More analysis of PSEP3 effects on plant growth can be obtained in the paper published in Nucleic Acid Research 8.
Satellite DNA (satDNA) constitutes a substantial part of eukaryotic genomes. In the last decade, it has been shown that satDNA is not an inert part of the genome and its function extends beyond the ...nuclear membrane. However, the number of model plant species suitable for studying the novel horizons of satDNA functionality is low. Here, we explored the satellitome of the model “basal” plant,
Physcomitrellapatens
(Hedwig, 1801) Bruch & Schimper, 1849 (moss), which has a number of advantages for deep functional and evolutionary research. Using a newly developed pyTanFinder pipeline (https://github.com/Kirovez/pyTanFinder) coupled with fluorescence
in situ
hybridization (FISH), we identified five high copy number tandem repeats (TRs) occupying a long DNA array in the moss genome. The nuclear organization study revealed that two TRs had distinct locations in the moss genome, concentrating in the heterochromatin and knob-rDNA like chromatin bodies. Further genomic, epigenetic and transcriptomic analysis showed that one TR, named PpNATR76, was located in the intergenic spacer (IGS) region and transcribed into long non-coding RNAs (lncRNAs). Several specific features of PpNATR76 lncRNAs make them very similar with the recently discovered human lncRNAs, raising a number of questions for future studies. This work provides new resources for functional studies of satellitome in plants using the model organism
P.patens
, and describes a list of tandem repeats for further analysis.
Nonsense-mediated mRNA decay (NMD) is a system that controls the quality of mRNA transcripts in eukaryotes by degradation of aberrant transcripts in a pioneer round of translation. In mammals, NMD ...targets one-third of mutated, disease-causing mRNAs and ∼10% of unmutated mRNAs, facilitating appropriate cellular responses to environmental changes 1. In plants, NMD plays an important role in development and regulating abiotic and biotic stress responses 2. The transcripts with premature termination codons (PTCs), upstream ORFs or long 3′-UTRs can be targeted to NMD. It was shown that alternative splicing plays a crucial role in regulation of NMD triggering, for example, by the introduction of a PTC in transcripts. Therefore, the correct identification of mRNA isoforms is a key step in the study of the principles of regulation of the cell transcriptome by the NMD pathway. Here, we performed long-read sequencing of Physcomitrella (Physcomitrium patens) mutant smg1Δ line 2 native transcriptome by Oxford Nanopore Technology (ONT). The smg1Δ is a knockout (KO) mutant deficient in SMG1 kinase is a key component of NMD system in plants and animals 3. RNA was isolated with Trizol from 5 day old protonemata and sequenced using kit SQK-RNA002, flow cells FLO-MIN106 and a MinION device (Oxford Nanopore Technologies Ltd., UK (ONT)) in three biological repeats. Basecalling was performed with Guppy v.4.0.15. The presented transcriptomes give advantages in the identification and functional characterization of RNA transcripts that are direct targets of the Nonsense-mediated mRNA decay system.
Nonsense-mediated RNA decay (NMD) mechanism controls the quality of eukaryotic mRNAs by degradation of aberrant transcripts with a premature stop codon (PTC) in a pioneer round of translation. ...Besides aberrant transcripts, up to 10% of normal mRNA transcripts can be regulated by NMD. As NMD machinery is associated with translation, this system takes part in proteome formation in eukaryotic cells 1,2. However, no proteomic datasets of plants with deficient NMD system are currently available.
Here, we provide an isobaric tag for relative and absolute quantitation (iTRAQ)-based quantitative proteomic dataset of the moss Physcomitrium patens smg1 knockout line. The kinase SMG1 is one of the key components of the NMD system in many organisms, including plants. 8-day old protonema of wild type and mutant lines was used for the iTRAQ experiment in three biological replicates. LC-MS/MS data were processed using PEAKS Studio v.8 Software with protein identification based on a Phytozome protein database. Differentially expressed protein groups up- and down-regulated in the smg1 knockout line were found in the resulting dataset. Presented data can improve our understanding of NMD functions in plants.
PDF
