Genome-Wide Analysis of the Lysine Biosynthesis Pathway Network during Maize Seed Development
Lysine is one of the most limiting essential amino acids for humans and livestock. The nutritional value of maize (Zea mays L.) is reduced by its poor lysine content. To better understand the lysine biosynthesis pathway in maize seed, we conducted a genome-wide analysis of the genes involved in lysi...
Gespeichert in:
| Veröffentlicht in: | PloS one 2016-02, Vol.11 (2), p.e0148287-e0148287 |
|---|---|
| Hauptverfasser: | , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | e0148287 |
|---|---|
| container_issue | 2 |
| container_start_page | e0148287 |
| container_title | PloS one |
| container_volume | 11 |
| creator | Liu, Yuwei Xie, Shaojun Yu, Jingjuan |
| description | Lysine is one of the most limiting essential amino acids for humans and livestock. The nutritional value of maize (Zea mays L.) is reduced by its poor lysine content. To better understand the lysine biosynthesis pathway in maize seed, we conducted a genome-wide analysis of the genes involved in lysine biosynthesis. We identified lysine biosynthesis pathway genes (LBPGs) and investigated whether a diaminopimelate pathway variant exists in maize. We analyzed two genes encoding the key enzyme dihydrodipicolinate synthase, and determined that they contribute differently to lysine synthesis during maize seed development. A coexpression network of LBPGs was constructed using RNA-sequencing data from 21 developmental stages of B73 maize seed. We found a large set of genes encoding ribosomal proteins, elongation factors and zein proteins that were coexpressed with LBPGs. The coexpressed genes were enriched in cellular metabolism terms and protein related terms. A phylogenetic analysis of the LBPGs from different plant species revealed different relationships. Additionally, six transcription factor (TF) families containing 13 TFs were identified as the Hub TFs of the LBPGs modules. Several expression quantitative trait loci of LBPGs were also identified. Our results should help to elucidate the lysine biosynthesis pathway network in maize seed. |
| doi_str_mv | 10.1371/journal.pone.0148287 |
| format | Article |
| fullrecord | <record><control><sourceid>gale_plos_</sourceid><recordid>TN_cdi_plos_journals_1761662948</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A442007527</galeid><doaj_id>oai_doaj_org_article_c839073275304a25b8a5a326878f3b98</doaj_id><sourcerecordid>A442007527</sourcerecordid><originalsourceid>FETCH-LOGICAL-c692t-cf80539b0f78fe5177b4b81ef959da393afa2b6ff18d27571b4368e7f5dd91513</originalsourceid><addsrcrecordid>eNqNk1tv0zAUxyMEYmPwDRBEQkLw0BLbiS8vSGXAqFQYYlyekOUkx627JC52slE-Pc6aTQ3aA8qD4-Pf-Z-LfaLoMUqmiDD0am0716hqurENTBOUcszZnegQCYInFCfk7t7_QfTA-3WSZIRTej86wJRjkWXkMPp5Ao2tYfLDlBDPgt7WGx9bHbcriBdh00D8xli_bYKhP_qs2tWl2safoL207jwuO2eaZfxRmT8QnwGU8Vu4gMpuamjah9E9rSoPj4b1KPr2_t3X4w-TxenJ_Hi2mBRU4HZSaB5SE3miGdeQIcbyNOcItMhEqYggSiucU60RLzHLGMpTQjkwnZWlQBkiR9HTne6msl4OnfESMYooxSLlgZjviNKqtdw4Uyu3lVYZeWWwbimVa01RgSw4EQkjIRBJUoWznKtMkdCykBzJRa_1eojW5TWURSjUqWokOj5pzEou7YVMGUkZ7QVeDALO_urAt7I2voCqUg3Y7ipvTFJKKAnos3_Q26sbqKUKBZhG2xC36EXlLE1xkrAMs0BNb6HCV0JtivCMtAn2kcPLkUNgWvjdLlXnvZyfffl_9vT7mH2-x65AVe3K26prjW38GEx3YOGs9w70TZNRIvspuO6G7KdADlMQ3J7sX9CN0_WzJ38BnwIA3A</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1761662948</pqid></control><display><type>article</type><title>Genome-Wide Analysis of the Lysine Biosynthesis Pathway Network during Maize Seed Development</title><source>Public Library of Science (PLoS) Journals Open Access</source><source>MEDLINE</source><source>DOAJ Directory of Open Access Journals</source><source>EZB-FREE-00999 freely available EZB journals</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><creator>Liu, Yuwei ; Xie, Shaojun ; Yu, Jingjuan</creator><creatorcontrib>Liu, Yuwei ; Xie, Shaojun ; Yu, Jingjuan</creatorcontrib><description>Lysine is one of the most limiting essential amino acids for humans and livestock. The nutritional value of maize (Zea mays L.) is reduced by its poor lysine content. To better understand the lysine biosynthesis pathway in maize seed, we conducted a genome-wide analysis of the genes involved in lysine biosynthesis. We identified lysine biosynthesis pathway genes (LBPGs) and investigated whether a diaminopimelate pathway variant exists in maize. We analyzed two genes encoding the key enzyme dihydrodipicolinate synthase, and determined that they contribute differently to lysine synthesis during maize seed development. A coexpression network of LBPGs was constructed using RNA-sequencing data from 21 developmental stages of B73 maize seed. We found a large set of genes encoding ribosomal proteins, elongation factors and zein proteins that were coexpressed with LBPGs. The coexpressed genes were enriched in cellular metabolism terms and protein related terms. A phylogenetic analysis of the LBPGs from different plant species revealed different relationships. Additionally, six transcription factor (TF) families containing 13 TFs were identified as the Hub TFs of the LBPGs modules. Several expression quantitative trait loci of LBPGs were also identified. Our results should help to elucidate the lysine biosynthesis pathway network in maize seed.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0148287</identifier><identifier>PMID: 26829553</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Amino acids ; Analysis ; Arabidopsis ; Arabidopsis thaliana ; Barley ; Biology and Life Sciences ; Biosynthesis ; Biosynthetic Pathways ; Computational Biology - methods ; Computer and Information Sciences ; Corn ; Dehydrogenases ; Developmental stages ; Dihydrodipicolinate synthase ; Elongation ; Enzymes ; Feedback ; Gene expression ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Plant ; Gene Regulatory Networks ; Gene sequencing ; Genes ; Genes, Plant ; Genetic aspects ; Genome-Wide Association Study ; Genomes ; Kinases ; Laboratories ; Livestock ; Lysine ; Lysine - biosynthesis ; Metabolism ; Molecular Sequence Annotation ; Nucleotide Motifs ; Phylogenetics ; Phylogeny ; Physical Sciences ; Physiological aspects ; Plant development ; Position-Specific Scoring Matrices ; Protein turnover ; Proteins ; Quantitative Trait Loci ; Regulatory Sequences, Nucleic Acid ; Research and Analysis Methods ; Ribonucleic acid ; Ribosomal proteins ; RNA ; Seeds ; Seeds - genetics ; Seeds - metabolism ; Transcription factors ; Zea mays ; Zea mays - genetics ; Zea mays - metabolism ; Zein</subject><ispartof>PloS one, 2016-02, Vol.11 (2), p.e0148287-e0148287</ispartof><rights>COPYRIGHT 2016 Public Library of Science</rights><rights>2016 Liu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2016 Liu et al 2016 Liu et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-cf80539b0f78fe5177b4b81ef959da393afa2b6ff18d27571b4368e7f5dd91513</citedby><cites>FETCH-LOGICAL-c692t-cf80539b0f78fe5177b4b81ef959da393afa2b6ff18d27571b4368e7f5dd91513</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4734768/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4734768/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79343,79344</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26829553$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Liu, Yuwei</creatorcontrib><creatorcontrib>Xie, Shaojun</creatorcontrib><creatorcontrib>Yu, Jingjuan</creatorcontrib><title>Genome-Wide Analysis of the Lysine Biosynthesis Pathway Network during Maize Seed Development</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Lysine is one of the most limiting essential amino acids for humans and livestock. The nutritional value of maize (Zea mays L.) is reduced by its poor lysine content. To better understand the lysine biosynthesis pathway in maize seed, we conducted a genome-wide analysis of the genes involved in lysine biosynthesis. We identified lysine biosynthesis pathway genes (LBPGs) and investigated whether a diaminopimelate pathway variant exists in maize. We analyzed two genes encoding the key enzyme dihydrodipicolinate synthase, and determined that they contribute differently to lysine synthesis during maize seed development. A coexpression network of LBPGs was constructed using RNA-sequencing data from 21 developmental stages of B73 maize seed. We found a large set of genes encoding ribosomal proteins, elongation factors and zein proteins that were coexpressed with LBPGs. The coexpressed genes were enriched in cellular metabolism terms and protein related terms. A phylogenetic analysis of the LBPGs from different plant species revealed different relationships. Additionally, six transcription factor (TF) families containing 13 TFs were identified as the Hub TFs of the LBPGs modules. Several expression quantitative trait loci of LBPGs were also identified. Our results should help to elucidate the lysine biosynthesis pathway network in maize seed.</description><subject>Amino acids</subject><subject>Analysis</subject><subject>Arabidopsis</subject><subject>Arabidopsis thaliana</subject><subject>Barley</subject><subject>Biology and Life Sciences</subject><subject>Biosynthesis</subject><subject>Biosynthetic Pathways</subject><subject>Computational Biology - methods</subject><subject>Computer and Information Sciences</subject><subject>Corn</subject><subject>Dehydrogenases</subject><subject>Developmental stages</subject><subject>Dihydrodipicolinate synthase</subject><subject>Elongation</subject><subject>Enzymes</subject><subject>Feedback</subject><subject>Gene expression</subject><subject>Gene Expression Regulation, Enzymologic</subject><subject>Gene Expression Regulation, Plant</subject><subject>Gene Regulatory Networks</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genes, Plant</subject><subject>Genetic aspects</subject><subject>Genome-Wide Association Study</subject><subject>Genomes</subject><subject>Kinases</subject><subject>Laboratories</subject><subject>Livestock</subject><subject>Lysine</subject><subject>Lysine - biosynthesis</subject><subject>Metabolism</subject><subject>Molecular Sequence Annotation</subject><subject>Nucleotide Motifs</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Physical Sciences</subject><subject>Physiological aspects</subject><subject>Plant development</subject><subject>Position-Specific Scoring Matrices</subject><subject>Protein turnover</subject><subject>Proteins</subject><subject>Quantitative Trait Loci</subject><subject>Regulatory Sequences, Nucleic Acid</subject><subject>Research and Analysis Methods</subject><subject>Ribonucleic acid</subject><subject>Ribosomal proteins</subject><subject>RNA</subject><subject>Seeds</subject><subject>Seeds - genetics</subject><subject>Seeds - metabolism</subject><subject>Transcription factors</subject><subject>Zea mays</subject><subject>Zea mays - genetics</subject><subject>Zea mays - metabolism</subject><subject>Zein</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNqNk1tv0zAUxyMEYmPwDRBEQkLw0BLbiS8vSGXAqFQYYlyekOUkx627JC52slE-Pc6aTQ3aA8qD4-Pf-Z-LfaLoMUqmiDD0am0716hqurENTBOUcszZnegQCYInFCfk7t7_QfTA-3WSZIRTej86wJRjkWXkMPp5Ao2tYfLDlBDPgt7WGx9bHbcriBdh00D8xli_bYKhP_qs2tWl2safoL207jwuO2eaZfxRmT8QnwGU8Vu4gMpuamjah9E9rSoPj4b1KPr2_t3X4w-TxenJ_Hi2mBRU4HZSaB5SE3miGdeQIcbyNOcItMhEqYggSiucU60RLzHLGMpTQjkwnZWlQBkiR9HTne6msl4OnfESMYooxSLlgZjviNKqtdw4Uyu3lVYZeWWwbimVa01RgSw4EQkjIRBJUoWznKtMkdCykBzJRa_1eojW5TWURSjUqWokOj5pzEou7YVMGUkZ7QVeDALO_urAt7I2voCqUg3Y7ipvTFJKKAnos3_Q26sbqKUKBZhG2xC36EXlLE1xkrAMs0BNb6HCV0JtivCMtAn2kcPLkUNgWvjdLlXnvZyfffl_9vT7mH2-x65AVe3K26prjW38GEx3YOGs9w70TZNRIvspuO6G7KdADlMQ3J7sX9CN0_WzJ38BnwIA3A</recordid><startdate>20160201</startdate><enddate>20160201</enddate><creator>Liu, Yuwei</creator><creator>Xie, Shaojun</creator><creator>Yu, Jingjuan</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20160201</creationdate><title>Genome-Wide Analysis of the Lysine Biosynthesis Pathway Network during Maize Seed Development</title><author>Liu, Yuwei ; Xie, Shaojun ; Yu, Jingjuan</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-cf80539b0f78fe5177b4b81ef959da393afa2b6ff18d27571b4368e7f5dd91513</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Amino acids</topic><topic>Analysis</topic><topic>Arabidopsis</topic><topic>Arabidopsis thaliana</topic><topic>Barley</topic><topic>Biology and Life Sciences</topic><topic>Biosynthesis</topic><topic>Biosynthetic Pathways</topic><topic>Computational Biology - methods</topic><topic>Computer and Information Sciences</topic><topic>Corn</topic><topic>Dehydrogenases</topic><topic>Developmental stages</topic><topic>Dihydrodipicolinate synthase</topic><topic>Elongation</topic><topic>Enzymes</topic><topic>Feedback</topic><topic>Gene expression</topic><topic>Gene Expression Regulation, Enzymologic</topic><topic>Gene Expression Regulation, Plant</topic><topic>Gene Regulatory Networks</topic><topic>Gene sequencing</topic><topic>Genes</topic><topic>Genes, Plant</topic><topic>Genetic aspects</topic><topic>Genome-Wide Association Study</topic><topic>Genomes</topic><topic>Kinases</topic><topic>Laboratories</topic><topic>Livestock</topic><topic>Lysine</topic><topic>Lysine - biosynthesis</topic><topic>Metabolism</topic><topic>Molecular Sequence Annotation</topic><topic>Nucleotide Motifs</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Physical Sciences</topic><topic>Physiological aspects</topic><topic>Plant development</topic><topic>Position-Specific Scoring Matrices</topic><topic>Protein turnover</topic><topic>Proteins</topic><topic>Quantitative Trait Loci</topic><topic>Regulatory Sequences, Nucleic Acid</topic><topic>Research and Analysis Methods</topic><topic>Ribonucleic acid</topic><topic>Ribosomal proteins</topic><topic>RNA</topic><topic>Seeds</topic><topic>Seeds - genetics</topic><topic>Seeds - metabolism</topic><topic>Transcription factors</topic><topic>Zea mays</topic><topic>Zea mays - genetics</topic><topic>Zea mays - metabolism</topic><topic>Zein</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Liu, Yuwei</creatorcontrib><creatorcontrib>Xie, Shaojun</creatorcontrib><creatorcontrib>Yu, Jingjuan</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Opposing Viewpoints in Context (Gale)</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Proquest Nursing & Allied Health Source</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - Academic</collection><collection>ProQuest Engineering Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Engineering Database</collection><collection>Nursing & Allied Health Premium</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>Materials Science Collection</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Liu, Yuwei</au><au>Xie, Shaojun</au><au>Yu, Jingjuan</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome-Wide Analysis of the Lysine Biosynthesis Pathway Network during Maize Seed Development</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2016-02-01</date><risdate>2016</risdate><volume>11</volume><issue>2</issue><spage>e0148287</spage><epage>e0148287</epage><pages>e0148287-e0148287</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Lysine is one of the most limiting essential amino acids for humans and livestock. The nutritional value of maize (Zea mays L.) is reduced by its poor lysine content. To better understand the lysine biosynthesis pathway in maize seed, we conducted a genome-wide analysis of the genes involved in lysine biosynthesis. We identified lysine biosynthesis pathway genes (LBPGs) and investigated whether a diaminopimelate pathway variant exists in maize. We analyzed two genes encoding the key enzyme dihydrodipicolinate synthase, and determined that they contribute differently to lysine synthesis during maize seed development. A coexpression network of LBPGs was constructed using RNA-sequencing data from 21 developmental stages of B73 maize seed. We found a large set of genes encoding ribosomal proteins, elongation factors and zein proteins that were coexpressed with LBPGs. The coexpressed genes were enriched in cellular metabolism terms and protein related terms. A phylogenetic analysis of the LBPGs from different plant species revealed different relationships. Additionally, six transcription factor (TF) families containing 13 TFs were identified as the Hub TFs of the LBPGs modules. Several expression quantitative trait loci of LBPGs were also identified. Our results should help to elucidate the lysine biosynthesis pathway network in maize seed.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>26829553</pmid><doi>10.1371/journal.pone.0148287</doi><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2016-02, Vol.11 (2), p.e0148287-e0148287 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1761662948 |
| source | Public Library of Science (PLoS) Journals Open Access; MEDLINE; DOAJ Directory of Open Access Journals; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Amino acids Analysis Arabidopsis Arabidopsis thaliana Barley Biology and Life Sciences Biosynthesis Biosynthetic Pathways Computational Biology - methods Computer and Information Sciences Corn Dehydrogenases Developmental stages Dihydrodipicolinate synthase Elongation Enzymes Feedback Gene expression Gene Expression Regulation, Enzymologic Gene Expression Regulation, Plant Gene Regulatory Networks Gene sequencing Genes Genes, Plant Genetic aspects Genome-Wide Association Study Genomes Kinases Laboratories Livestock Lysine Lysine - biosynthesis Metabolism Molecular Sequence Annotation Nucleotide Motifs Phylogenetics Phylogeny Physical Sciences Physiological aspects Plant development Position-Specific Scoring Matrices Protein turnover Proteins Quantitative Trait Loci Regulatory Sequences, Nucleic Acid Research and Analysis Methods Ribonucleic acid Ribosomal proteins RNA Seeds Seeds - genetics Seeds - metabolism Transcription factors Zea mays Zea mays - genetics Zea mays - metabolism Zein |
| title | Genome-Wide Analysis of the Lysine Biosynthesis Pathway Network during Maize Seed Development |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-01T17%3A39%3A06IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Genome-Wide%20Analysis%20of%20the%20Lysine%20Biosynthesis%20Pathway%20Network%20during%20Maize%20Seed%20Development&rft.jtitle=PloS%20one&rft.au=Liu,%20Yuwei&rft.date=2016-02-01&rft.volume=11&rft.issue=2&rft.spage=e0148287&rft.epage=e0148287&rft.pages=e0148287-e0148287&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0148287&rft_dat=%3Cgale_plos_%3EA442007527%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1761662948&rft_id=info:pmid/26829553&rft_galeid=A442007527&rft_doaj_id=oai_doaj_org_article_c839073275304a25b8a5a326878f3b98&rfr_iscdi=true |