On the public citation graph

The Phaeodactylum tricornutum Diaminopimelate Decarboxylase was Acquired via Horizontal Gene Transfer from Bacteria and Displays Substrate Promiscuity

https://doi.org/10.1101/2020.10.01.322594

0 signed · 89 inferred · view as graph

Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.

Is this your work? Sign in with ORCID and put your name on the claims that are yours.

Claim with ORCID

Reference health. See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.

See reference health

What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/978-1-60327-058-8_14openalex-snapshot

High Throughput Production of Recombinant Human Proteins for Crystallography

inferredcites →https://doi.org/10.1007/bf00027077openalex-snapshot

Regulation of lysine synthesis in transgenic potato plants expressing a bacterial dihydrodipicolinate synthase in their chloroplasts

inferredcites →https://doi.org/10.1007/bf02172403openalex-snapshot

Stable nuclear transformation of the diatomPhaeodactylum tricornutum

inferredcites →https://doi.org/10.1007/s00239-002-2340-2openalex-snapshot

Molecular Evolution of the Lysine Biosynthetic Pathways

inferredcites →https://doi.org/10.1007/s00726-004-0118-0openalex-snapshot

Marfey?s reagent for chiral amino acid analysis: A review

inferredcites →https://doi.org/10.1007/s10969-009-9065-zopenalex-snapshot

The three-dimensional structure of diaminopimelate decarboxylase from Mycobacterium tuberculosis reveals a tetrameric enzyme organisation

inferredcites →https://doi.org/10.1016/0014-5793(80)80640-5openalex-snapshot

The enzymology of lysine biosynthesis in higher plants

inferredcites →https://doi.org/10.1016/j.bbagen.2004.09.008openalex-snapshot

Biosynthesis of lysine in plants: evidence for a variant of the known bacterial pathways

inferredcites →https://doi.org/10.1016/j.bbrc.2017.11.097openalex-snapshot

Structural basis for substrate specificity of meso-diaminopimelic acid decarboxylase from Corynebacterium glutamicum

inferredcites →https://doi.org/10.1016/j.biochi.2013.06.026openalex-snapshot

A new robust kinetic assay for DAP epimerase activity

inferredcites →https://doi.org/10.1016/j.biochi.2015.05.004openalex-snapshot

An optimized coupled assay for quantifying diaminopimelate decarboxylase activity

inferredcites →https://doi.org/10.1016/j.gene.2007.05.022openalex-snapshot

Molecular toolbox for studying diatom biology in Phaeodactylum tricornutum

inferredcites →https://doi.org/10.1016/j.jsb.2010.06.008openalex-snapshot

High-throughput production of human proteins for crystallization: The SGC experience

inferredcites →https://doi.org/10.1016/s0969-2126(02)00880-8openalex-snapshot

Cocrystal Structures of Diaminopimelate Decarboxylase

inferredcites →https://doi.org/10.1016/s0969-2126(99)80073-2openalex-snapshot

Structure of mammalian ornithine decarboxylase at 1.6 Å resolution: stereochemical implications of PLP-dependent amino acid decarboxylases

inferredcites →https://doi.org/10.1021/bi00030a002openalex-snapshot

Crystal Structure of a D-Amino Acid Aminotransferase: How the Protein Controls Stereoselectivity

inferredcites →https://doi.org/10.1021/bi00334a028openalex-snapshot

Stereochemistry of lysine formation by meso-diaminopimelate decarboxylase from wheat germ: use of proton-carbon-13 NMR shift correlation to detect stereospecific deuterium labeling

inferredcites →https://doi.org/10.1021/bi00527a022openalex-snapshot

Stereochemistry of meso-.alpha.,.epsilon.-diaminopimelate decarboxylase reaction: the first evidence for pyridoxal 5'-phosphate dependent decarboxylation with inversion of configuration

inferredcites →https://doi.org/10.1038/169533a0openalex-snapshot

Diaminopimelic Acid and Lysine: Diaminopimelic Acid Decarboxylase

inferredcites →https://doi.org/10.1038/nature07410openalex-snapshot

The Phaeodactylum genome reveals the evolutionary history of diatom genomes

inferredcites →https://doi.org/10.1038/nature08057openalex-snapshot

The life of diatoms in the world's oceans

inferredcites →https://doi.org/10.1038/nature10074openalex-snapshot

Evolution and metabolic significance of the urea cycle in photosynthetic diatoms

inferredcites →https://doi.org/10.1038/nature20803openalex-snapshot

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus

inferredcites →https://doi.org/10.1038/nbt.3988openalex-snapshot

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

inferredcites →https://doi.org/10.1038/ncomms1738openalex-snapshot

Structure-guided evolution of cyan fluorescent proteins towards a quantum yield of 93%

inferredcites →https://doi.org/10.1038/ncomms7925openalex-snapshot

Designer diatom episomes delivered by bacterial conjugation

inferredcites →https://doi.org/10.1038/nmeth.3176openalex-snapshot

Fast and sensitive protein alignment using DIAMOND

inferredcites →https://doi.org/10.1038/nprot.2007.321openalex-snapshot

The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability

inferredcites →https://doi.org/10.1038/s41467-018-07563-6openalex-snapshot

Widespread bacterial lysine degradation proceeding via glutarate and L-2-hydroxyglutarate

inferredcites →https://doi.org/10.1038/s41467-019-12407-yopenalex-snapshot

Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom

inferredcites →https://doi.org/10.1038/srep00955openalex-snapshot

Plastid-localized amino acid biosynthetic pathways of Plantae are predominantly composed of non-cyanobacterial enzymes

inferredcites →https://doi.org/10.1038/srep42318openalex-snapshot

Structural basis for redox sensitivity in Corynebacterium glutamicum diaminopimelate epimerase: an enzyme involved in l-lysine biosynthesis

inferredcites →https://doi.org/10.1039/b705624aopenalex-snapshot

Inhibition of lysine biosynthesis: an evolving antibiotic strategy

inferredcites →https://doi.org/10.1042/bj0960075openalex-snapshot

PURIFICATION AND PROPERTIES OF DIAMINOPIMELATE DECARBOXYLASE FROM ESCHERICHIA COLI

inferredcites →https://doi.org/10.1046/j.1529-8817.1999.3520368.xopenalex-snapshot

BOLIDOMONAS : A NEW GENUS WITH TWO SPECIES BELONGING TO A NEW ALGAL CLASS, THE BOLIDOPHYCEAE (HETEROKONTA)

inferredcites →https://doi.org/10.1073/pnas.0608643103openalex-snapshot

l , l -diaminopimelate aminotransferase, a trans-kingdom enzyme shared by Chlamydia and plants for synthesis of diaminopimelate/lysine

inferredcites →https://doi.org/10.1073/pnas.0811011106openalex-snapshot

One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome

inferredcites →https://doi.org/10.1073/pnas.1319773111openalex-snapshot

Mapping the diatom redox-sensitive proteome provides insight into response to nitrogen stress in the marine environment

inferredcites →https://doi.org/10.1074/jbc.m115.696591openalex-snapshot

Dimerization of Bacterial Diaminopimelate Decarboxylase Is Essential for Catalysis

inferredcites →https://doi.org/10.1074/jbc.m301549200openalex-snapshot

Crystal Structure of Mycobacterium tuberculosis Diaminopimelate Decarboxylase, an Essential Enzyme in Bacterial Lysine Biosynthesis

inferredcites →https://doi.org/10.1074/jbc.m801823200openalex-snapshot

The Catalytic Intermediate Stabilized by a “Down” Active Site Loop for Diaminopimelate Decarboxylase from Helicobacter pylori

inferredcites →https://doi.org/10.1074/jbc.ra118.006825openalex-snapshot

Structure–function analyses of two plant meso-diaminopimelate decarboxylase isoforms reveal that active-site gating provides stereochemical control

inferredcites →https://doi.org/10.1089/mdr.1999.5.163openalex-snapshot

Antibiotic Resistance As a Stress Response: Complete Sequencing of a Large Number of Chromosomal Loci in Staphylococcus aureus Strain COL That Impact on the Expression of Resistance to Methicillin

inferredcites →https://doi.org/10.1093/bioinformatics/btp348openalex-snapshot

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

inferredcites →https://doi.org/10.1093/jxb/eri161openalex-snapshot

Chloroplasts as source and target of cellular redox regulation: a discussion on chloroplast redox signals in the context of plant physiology

inferredcites →https://doi.org/10.1093/jxb/ers119openalex-snapshot

The multifaceted role of aspartate-family amino acids in plant metabolism

inferredcites →https://doi.org/10.1093/jxb/eru320openalex-snapshot

Regulation of amino acid metabolic enzymes and transporters in plants

inferredcites →https://doi.org/10.1093/molbev/msl133openalex-snapshot

Functional Classification of Amino Acid Decarboxylases from the Alanine Racemase Structural Family by Phylogenetic Studies

inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

inferredcites →https://doi.org/10.1093/molbev/msu300openalex-snapshot

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

inferredcites →https://doi.org/10.1093/nar/gkp448openalex-snapshot

Gene silencing in the marine diatom Phaeodactylum tricornutum

inferredcites →https://doi.org/10.1093/sysbio/syt022openalex-snapshot

PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment

inferredcites →https://doi.org/10.1093/sysbio/syx068openalex-snapshot

Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation

inferredcites →https://doi.org/10.1098/rstb.2016.0402openalex-snapshot

Intracellular metabolic pathway distribution in diatoms and tools for genome-enabled experimental diatom research

inferredcites →https://doi.org/10.1101/gr.849004openalex-snapshot

WebLogo: A Sequence Logo Generator: Figure 1

inferredcites →https://doi.org/10.1104/pp.103.037168openalex-snapshot

Lysine Metabolism Is Concurrently Regulated by Synthesis and Catabolism in Both Reproductive and Vegetative Tissues

inferredcites →https://doi.org/10.1104/pp.105.072629openalex-snapshot

An ll -Diaminopimelate Aminotransferase Defines a Novel Variant of the Lysine Biosynthesis Pathway in Plants

inferredcites →https://doi.org/10.1104/pp.65.6.1166openalex-snapshot

Photosynthetic Formation of the Aspartate Family of Amino Acids in Isolated Chloroplasts

inferredcites →https://doi.org/10.1107/s0021889807021206openalex-snapshot

Phaser crystallographic software

inferredcites →https://doi.org/10.1107/s0907444904019158openalex-snapshot

Coot : model-building tools for molecular graphics

inferredcites →https://doi.org/10.1107/s0907444906022116openalex-snapshot

The Buccaneer software for automated model building. 1. Tracing protein chains

inferredcites →https://doi.org/10.1107/s0907444909042073openalex-snapshot

MolProbity : all-atom structure validation for macromolecular crystallography

inferredcites →https://doi.org/10.1107/s0907444910045749openalex-snapshot

Overview of the CCP 4 suite and current developments

inferredcites →https://doi.org/10.1107/s0907444994003112openalex-snapshot

The CCP4 suite: programs for protein crystallography

inferredcites →https://doi.org/10.1107/s2059798319011471openalex-snapshot

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

inferredcites →https://doi.org/10.1111/j.1365-313x.2004.02294.xopenalex-snapshot

Identification and characterization of a new conserved motif within the presequence of proteins targeted into complex diatom plastids

inferredcites →https://doi.org/10.1111/j.1471-4159.1978.tb06536.xopenalex-snapshot

LYSINE METABOLISM IN THE RAT BRAIN: THE PIPECOLIC ACID‐FORMING PATHWAY

inferredcites →https://doi.org/10.1111/j.1574-6968.1998.tb13341.xopenalex-snapshot

Lysine is synthesized through the α-aminoadipate pathway inThermus thermophilus

inferredcites →https://doi.org/10.1111/j.1742-4658.2005.04760.xopenalex-snapshot

A new molecular tool for transgenic diatoms

inferredcites →https://doi.org/10.1111/nph.15625openalex-snapshot

Loop assembly: a simple and open system for recursive fabrication of DNA circuits

inferredcites →https://doi.org/10.1111/pbi.12254openalex-snapshot

Inactivation of P haeodactylum tricornutum urease gene using transcription activator‐like effector nuclease‐based targeted mutagenesis

inferredcites →https://doi.org/10.1126/science.1101156openalex-snapshot

The Genome of the Diatom Thalassiosira Pseudonana : Ecology, Evolution, and Metabolism

inferredcites →https://doi.org/10.1126/science.aau0382openalex-snapshot

Biosynthesis of the neurotoxin domoic acid in a bloom-forming diatom

inferredcites →https://doi.org/10.1128/jb.105.3.844-854.1971openalex-snapshot

Genetic Analysis of Diaminopimelic Acid- and Lysine-Requiring Mutants of Escherichia coli

inferredcites →https://doi.org/10.1146/annurev-marine-120308-081051openalex-snapshot

Oceanographic and Biogeochemical Insights from Diatom Genomes

inferredcites →https://doi.org/10.1186/s12864-015-1574-5openalex-snapshot

Key genes as stress indicators in the ubiquitous diatom Skeletonema marinoi

inferredcites →https://doi.org/10.1199/tab.0121openalex-snapshot

Aspartate-Derived Amino Acid Biosynthesis inArabidopsis thaliana

inferredcites →https://doi.org/10.1242/jcs.00092openalex-snapshot

In vivo characterization of diatom multipartite plastid targeting signals

inferredcites →https://doi.org/10.1371/journal.pgen.1006490openalex-snapshot

Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation

inferredcites →https://doi.org/10.1371/journal.pgen.1007147openalex-snapshot

Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics

inferredcites →https://doi.org/10.1371/journal.pone.0035968openalex-snapshot

Possible Role of Horizontal Gene Transfer in the Colonization of Sea Ice by Algae

inferredcites →https://doi.org/10.1371/journal.pone.0040318openalex-snapshot

Characterisation of the First Enzymes Committed to Lysine Biosynthesis in Arabidopsis thaliana

inferredcites →https://doi.org/10.1371/journal.pone.0090372openalex-snapshot

A New and Improved Host-Independent Plasmid System for RK2-Based Conjugal Transfer

inferredcites →https://doi.org/10.1385/cbb:46:1:43openalex-snapshot

The α-Aminoadipate Pathway for Lysine Biosynthesis in Fungi

inferredcites →https://doi.org/10.3389/fbioe.2016.00065openalex-snapshot

Refinement of the Diatom Episome Maintenance Sequence and Improvement of Conjugation-Based DNA Delivery Methods

inferredcites →https://doi.org/10.3389/fmicb.2020.00005openalex-snapshot

Multiplexed Knockouts in the Model Diatom Phaeodactylum by Episomal Delivery of a Selectable Cas9

inferredcites →https://doi.org/10.3390/metabo3020294openalex-snapshot

Amino Acid Biosynthesis Pathways in Diatoms

inferredcites →https://doi.org/10.7717/peerj.2344openalex-snapshot

Rapid induction of GFP expression by the nitrate reductase promoter in the diatomPhaeodactylum tricornutum

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1021/acssynbio.3c00163openalex-snapshot

Validating a Promoter Library for Application in Plasmid-Based Diatom Genetic Engineering

Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.