Genome-Wide Analysis of the Lysine Biosynthesis Pathway Network during Maize Seed Development

PloS One
Yuwei LiuJingjuan Yu

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 wer...Continue Reading

References

Jan 1, 1990·Proceedings of the National Academy of Sciences of the United States of America·R J SchmidtB Burr
Sep 12, 1995·Proceedings of the National Academy of Sciences of the United States of America·J E HabbenB A Larkins
Mar 29, 1994·Proceedings of the National Academy of Sciences of the United States of America·H KarchiG Galili
Mar 27, 1998·Nature·N McLennan, M Masters
Jun 6, 1998·Proceedings of the National Academy of Sciences of the United States of America·T IshidaS Sano
Jun 1, 1995·Bio/technology·S C FalcoP Webber
Jan 5, 1999·Bioorganic & Medicinal Chemistry Letters·L D GegnasK K Wong
Mar 30, 2002·Science·Rachel B BremLeonid Kruglyak
Jul 1, 1995·The Plant Cell·G. Galili
Oct 2, 2002·Journal of Molecular Evolution·A M VelascoA Lazcano
Dec 12, 2002·Trends in Plant Science·Shuichi Yanagisawa
Mar 21, 2003·Nature·Eric E SchadtStephen H Friend
Nov 5, 2003·Development·Thomas KrojFrançois Parcy
Jan 22, 2004·Nature Reviews. Genetics·Albert-László Barabási, Zoltán N Oltvai
Mar 9, 2004·Current Opinion in Plant Biology·Pierre Broun
Jun 3, 2004·Genome Research·Elizabeth J B Williams, Dianna J Bowles
Jul 23, 2004·Nature·Michael MorleyVivian G Cheung
May 2, 2006·Statistical Applications in Genetics and Molecular Biology·Bin Zhang, Steve Horvath
Jul 18, 2006·Nucleic Acids Research·Jia YeJun Wang
Sep 1, 2006·Cell Biochemistry and Biophysics·Hengyu XuPaul F Cook
Dec 7, 2006·Plant Biotechnology Journal·Shihshieh HuangMichael H Luethy
Nov 23, 2007·BMC Systems Biology·Peter Langfelder, Steve Horvath
Jun 3, 2008·Nature Methods·Ali MortazaviBarbara Wold
Jul 4, 2008·Trends in Genetics : TIG·Yoav GiladJonathan K Pritchard
Aug 15, 2008·Plant & Cell Physiology·Jérôme Verdier, Richard D Thompson
Nov 19, 2008·Nature Reviews. Genetics·Zhong WangMichael Snyder
Dec 31, 2008·BMC Bioinformatics·Peter Langfelder, Steve Horvath
Dec 8, 2009·Science·Patrick S SchnableRichard K Wilson
Mar 12, 2010·Nature·Stephen B MontgomeryEmmanouil T Dermitzakis
Apr 2, 2010·BMC Bioinformatics·Robert C McLeay, Timothy L Bailey
Dec 21, 2010·American Journal of Human Genetics·Jian YangPeter M Visscher
Feb 15, 2011·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Pinky AgarwalAkhilesh K Tyagi

❮ Previous
Next ❯

Citations

Jul 5, 2021·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Langlang MaYaou Shen

❮ Previous
Next ❯

Methods Mentioned

BETA
RNA-Seq
PCR
immunoprecipitation
aminoacylation

Software Mentioned

GAPIT
WEGO
PLINK
BLASTP
GCTA
custom Perl script
MEME
Cytoscape
Genomic Association and Prediction Integrated Tool ( GAPIT )
Phytozome

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.