Differential Analysis of Proteomes and Metabolomes Reveals Additively Balanced Networking for Metabolism in Maize Heterosis

A century ago, dominance and overdominance hypotheses were developed to explain the phenomenon of heterosis, both hypotheses were in a nonadditive pattern. Here, a principal component analysis (PCA) of maize seed proteomes was used for representative inbreds of five heterotic germplasms and three classes of hybrid. Hybrids congregated in the center region of inbreds, forming an additive distribution with hybrids in the middle of their parents. Principal components 1 and 2 indicated biased distributions of proteins with functions of amino acid–protein or carbohydrate–energy metabolisms, respectively, after loading analysis and MS identification of proteins. Then, GC–MS was used to examine free amino acids, carbohydrates, and organic acids. A lower level of these metabolites were found in hybrids than inbreds. Further, we performed similar analyses of germinating seeds of a parent–F1 triad and three F2 segregants and confirmed these results. Therefore, an additive pattern of protein abundances for an unimpeded flow of metabolites was established in heterotic hybrids. That is, an additively balanced networking but not the nonadditive dominance or overdominance regulates heterosis. The less expensive metabolism in hybrids suggested the evolution of sexual reproduction. The Mendelian phenotypic ratio can be better explained based on this additive pattern than dominance

Proteomic Analysis Reveals an Aflatoxin-Triggered Immune Response in Cotyledons of <i>Arachis hypogaea</i> Infected with <i>Aspergillus flavus</i>

An immune response is triggered in host cells when host receptors recognize conserved molecular motifs, pathogen-associated molecular patterns (PAMPs), such as β-glucans, and chitin at the cell surface of a pathogen. Effector-triggered immunity occurs when pathogens deliver effectors into the host cell to suppress the first immune signaling. Using a differential proteomic approach, we identified an array of proteins responding to aflatoxins in cotyledons of peanut (<i>Arachis hypogaea</i>) infected with aflatoxin-producing (toxigenic) but not nonaflatoxin-producing (atoxigenic) strains of <i>Aspergillus flavus</i>. These proteins are involved in immune signaling and PAMP perception, DNA and RNA stabilization, induction of defense, innate immunity, hypersensitive response, biosynthesis of phytoalexins, cell wall responses, peptidoglycan assembly, penetration resistance, condensed tannin synthesis, detoxification, and metabolic regulation. Gene expression analysis confirmed the differential abundance of proteins in peanut cotyledons supplemented with aflatoxins, with or without infection with the atoxigenic strain. Similarly, peanut germination and <i>A. flavus</i> growth were altered in response to aflatoxin B1. These findings show an additional immunity initiated by aflatoxins. With the PAMP- and effector-triggered immune responses, this immunity constitutes the third immune response of the immune system in peanut cotyledon cells. The system is also a three-grade coevolution of plant–pathogen interaction

Proteomic Analysis Reveals an Aflatoxin-Triggered Immune Response in Cotyledons of <i>Arachis hypogaea</i> Infected with <i>Aspergillus flavus</i>

An immune response is triggered in host cells when host receptors recognize conserved molecular motifs, pathogen-associated molecular patterns (PAMPs), such as β-glucans, and chitin at the cell surface of a pathogen. Effector-triggered immunity occurs when pathogens deliver effectors into the host cell to suppress the first immune signaling. Using a differential proteomic approach, we identified an array of proteins responding to aflatoxins in cotyledons of peanut (<i>Arachis hypogaea</i>) infected with aflatoxin-producing (toxigenic) but not nonaflatoxin-producing (atoxigenic) strains of <i>Aspergillus flavus</i>. These proteins are involved in immune signaling and PAMP perception, DNA and RNA stabilization, induction of defense, innate immunity, hypersensitive response, biosynthesis of phytoalexins, cell wall responses, peptidoglycan assembly, penetration resistance, condensed tannin synthesis, detoxification, and metabolic regulation. Gene expression analysis confirmed the differential abundance of proteins in peanut cotyledons supplemented with aflatoxins, with or without infection with the atoxigenic strain. Similarly, peanut germination and <i>A. flavus</i> growth were altered in response to aflatoxin B1. These findings show an additional immunity initiated by aflatoxins. With the PAMP- and effector-triggered immune responses, this immunity constitutes the third immune response of the immune system in peanut cotyledon cells. The system is also a three-grade coevolution of plant–pathogen interaction

Proteomic Analysis Reveals an Aflatoxin-Triggered Immune Response in Cotyledons of <i>Arachis hypogaea</i> Infected with <i>Aspergillus flavus</i>

An immune response is triggered in host cells when host receptors recognize conserved molecular motifs, pathogen-associated molecular patterns (PAMPs), such as β-glucans, and chitin at the cell surface of a pathogen. Effector-triggered immunity occurs when pathogens deliver effectors into the host cell to suppress the first immune signaling. Using a differential proteomic approach, we identified an array of proteins responding to aflatoxins in cotyledons of peanut (<i>Arachis hypogaea</i>) infected with aflatoxin-producing (toxigenic) but not nonaflatoxin-producing (atoxigenic) strains of <i>Aspergillus flavus</i>. These proteins are involved in immune signaling and PAMP perception, DNA and RNA stabilization, induction of defense, innate immunity, hypersensitive response, biosynthesis of phytoalexins, cell wall responses, peptidoglycan assembly, penetration resistance, condensed tannin synthesis, detoxification, and metabolic regulation. Gene expression analysis confirmed the differential abundance of proteins in peanut cotyledons supplemented with aflatoxins, with or without infection with the atoxigenic strain. Similarly, peanut germination and <i>A. flavus</i> growth were altered in response to aflatoxin B1. These findings show an additional immunity initiated by aflatoxins. With the PAMP- and effector-triggered immune responses, this immunity constitutes the third immune response of the immune system in peanut cotyledon cells. The system is also a three-grade coevolution of plant–pathogen interaction

Proteomic Analysis Reveals an Aflatoxin-Triggered Immune Response in Cotyledons of <i>Arachis hypogaea</i> Infected with <i>Aspergillus flavus</i>

An immune response is triggered in host cells when host receptors recognize conserved molecular motifs, pathogen-associated molecular patterns (PAMPs), such as β-glucans, and chitin at the cell surface of a pathogen. Effector-triggered immunity occurs when pathogens deliver effectors into the host cell to suppress the first immune signaling. Using a differential proteomic approach, we identified an array of proteins responding to aflatoxins in cotyledons of peanut (<i>Arachis hypogaea</i>) infected with aflatoxin-producing (toxigenic) but not nonaflatoxin-producing (atoxigenic) strains of <i>Aspergillus flavus</i>. These proteins are involved in immune signaling and PAMP perception, DNA and RNA stabilization, induction of defense, innate immunity, hypersensitive response, biosynthesis of phytoalexins, cell wall responses, peptidoglycan assembly, penetration resistance, condensed tannin synthesis, detoxification, and metabolic regulation. Gene expression analysis confirmed the differential abundance of proteins in peanut cotyledons supplemented with aflatoxins, with or without infection with the atoxigenic strain. Similarly, peanut germination and <i>A. flavus</i> growth were altered in response to aflatoxin B1. These findings show an additional immunity initiated by aflatoxins. With the PAMP- and effector-triggered immune responses, this immunity constitutes the third immune response of the immune system in peanut cotyledon cells. The system is also a three-grade coevolution of plant–pathogen interaction

Proteomic Analysis Reveals an Aflatoxin-Triggered Immune Response in Cotyledons of <i>Arachis hypogaea</i> Infected with <i>Aspergillus flavus</i>

An immune response is triggered in host cells when host receptors recognize conserved molecular motifs, pathogen-associated molecular patterns (PAMPs), such as β-glucans, and chitin at the cell surface of a pathogen. Effector-triggered immunity occurs when pathogens deliver effectors into the host cell to suppress the first immune signaling. Using a differential proteomic approach, we identified an array of proteins responding to aflatoxins in cotyledons of peanut (<i>Arachis hypogaea</i>) infected with aflatoxin-producing (toxigenic) but not nonaflatoxin-producing (atoxigenic) strains of <i>Aspergillus flavus</i>. These proteins are involved in immune signaling and PAMP perception, DNA and RNA stabilization, induction of defense, innate immunity, hypersensitive response, biosynthesis of phytoalexins, cell wall responses, peptidoglycan assembly, penetration resistance, condensed tannin synthesis, detoxification, and metabolic regulation. Gene expression analysis confirmed the differential abundance of proteins in peanut cotyledons supplemented with aflatoxins, with or without infection with the atoxigenic strain. Similarly, peanut germination and <i>A. flavus</i> growth were altered in response to aflatoxin B1. These findings show an additional immunity initiated by aflatoxins. With the PAMP- and effector-triggered immune responses, this immunity constitutes the third immune response of the immune system in peanut cotyledon cells. The system is also a three-grade coevolution of plant–pathogen interaction

Proteomics Insight into the Biological Safety of Transgenic Modification of Rice As Compared with Conventional Genetic Breeding and Spontaneous Genotypic Variation

The potential of unintended effects caused by transgenic events is a key issue in the commercialization of genetically modified (GM) crops. To investigate whether transgenic events cause unintended effects, we used comparative proteomics approaches to evaluate proteome differences in seeds from 2 sets of GM <i>indica</i> rice, herbicide-resistant Bar68-1 carrying <i>bar</i> and insect-resistant 2036-1a carrying <i>cry1Ac</i>/<i>sck</i>, and their respective controls D68 and MH86, as well as <i>indica</i> variety MH63, a parental line for breeding MH86, and <i>japonica</i> variety ZH10. This experimental design allowed for comparing proteome difference caused by transgenes, conventional genetic breeding, and natural genetic variation. Proteomics analysis revealed the maximum numbers of differentially expressed proteins between <i>indica</i> and <i>japonica</i> cultivars, second among <i>indica</i> varieties with relative small difference between MH86 and MH63, and the minimum between GM rice and respective control, thus indicating GM events do not substantially alter proteome profiles as compared with conventional genetic breeding and natural genetic variation. Mass spectrometry analysis revealed 234 proteins differentially expressed in the 6 materials, and these proteins were involved in different cellular and metabolic processes with a prominent skew toward metabolism (31.2%), protein synthesis and destination (25.2%), and defense response (22.4%). In these seed proteomes, proteins implicated in the 3 prominent biological processes showed significantly different composite expression patterns and were major factors differentiating <i>japonica</i> and <i>indica</i> cultivars, as well as <i>indica</i> varieties. Thus, metabolism, protein synthesis and destination, and defense response in seeds are important in differentiating rice cultivars and varieties

Proteomics Insight into the Biological Safety of Transgenic Modification of Rice As Compared with Conventional Genetic Breeding and Spontaneous Genotypic Variation

The potential of unintended effects caused by transgenic events is a key issue in the commercialization of genetically modified (GM) crops. To investigate whether transgenic events cause unintended effects, we used comparative proteomics approaches to evaluate proteome differences in seeds from 2 sets of GM <i>indica</i> rice, herbicide-resistant Bar68-1 carrying <i>bar</i> and insect-resistant 2036-1a carrying <i>cry1Ac</i>/<i>sck</i>, and their respective controls D68 and MH86, as well as <i>indica</i> variety MH63, a parental line for breeding MH86, and <i>japonica</i> variety ZH10. This experimental design allowed for comparing proteome difference caused by transgenes, conventional genetic breeding, and natural genetic variation. Proteomics analysis revealed the maximum numbers of differentially expressed proteins between <i>indica</i> and <i>japonica</i> cultivars, second among <i>indica</i> varieties with relative small difference between MH86 and MH63, and the minimum between GM rice and respective control, thus indicating GM events do not substantially alter proteome profiles as compared with conventional genetic breeding and natural genetic variation. Mass spectrometry analysis revealed 234 proteins differentially expressed in the 6 materials, and these proteins were involved in different cellular and metabolic processes with a prominent skew toward metabolism (31.2%), protein synthesis and destination (25.2%), and defense response (22.4%). In these seed proteomes, proteins implicated in the 3 prominent biological processes showed significantly different composite expression patterns and were major factors differentiating <i>japonica</i> and <i>indica</i> cultivars, as well as <i>indica</i> varieties. Thus, metabolism, protein synthesis and destination, and defense response in seeds are important in differentiating rice cultivars and varieties