Genomic DNA Sequences that Encode for Herbicide Targets.
This database was created to (1) give quick access to the most common herbicide resistance genes across a wide range of weedy species and (2) provide a resource for researchers interested in discovering these gene sequences from weed species not listed here. See the notes below the table to find tools that may be useful for the latter objective.
Darci Giacomini is the curator of this information. She is affiliated with the University of Illinois and Monsanto. University of Illinois 320 ERML 1201 W. Gregory Drive Urbana, IL 61801 dagiac@illinois.edu
To add a new sequence, add further information to an existing case, point out an error, or just comment please click here.
SEE NOTES INCLUDING A DISCLAIMER AND T-COFFEE BELOW THE TABLE FOR A DEFINITION OF THE TARGETS
NOTES
The targets are:
EPSPS - 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase is an enzyme that catalyzes the chemical reaction: phosphoenolpyruvate + 3-phosphoshikimate <----> phosphate + 5-enolpyruvylshikimate-3-phosphate (EPSP).
GS - Glutamine synthetase is an enzyme that plays an essential role in the metabolism of nitrogen by catalyzing the condensation of glutamate and ammonia to form glutamine: Glutamate + ATP + NH3 → Glutamine + ADP + phosphate
ACCase - Acetyl-CoA carboxylase is a biotin-dependent enzyme that catalyzes the irreversible carboxylation of acetyl-CoA to produce malonyl-CoA through its two catalytic activities, biotin carboxylase (BC) and carboxyltransferase (CT).
ALS - acetolactate synthase (ALS) enzyme (also known as acetohydroxy acid synthase, or AHAS) catalyzes the first step in the synthesis of the branched-chain amino acids (valine, leucine, and isoleucine).
HPPD - 4-Hydroxyphenylpyruvate dioxygenase is an enzyme found in both plants and animals which catalyzes the catabolism of the amino acid tyrosine.
PDS - Phytoene desaturase is an enzyme required in the biosynthesis of carotenoids which inturn play an important role in dissipating the oxidative energy of singlet O2 (1O2).
PPO - Protoporphyrinogen oxidase (PPG oxidase or Protox) is an enzyme of chlorophyll and heme biosynthesis catalyzing the oxidation of protoporphyrinogen IX (PPGIX) to protoporphyrin IX (PPIX).
T-Coffee (Tree-based Consistency Objective Function For alignment Evaluation) is a multiple sequence alignment software. It generates a library of pairwise alignments to guide the multiple sequence alignment.
Please cite these results as: Giacomini,D., Heap, I., and Sammons, R.D. T-Coffee Alignments of Herbicide Target Genes.
Click on the following links to see T-Coffee alignment for these targets:
EPSPS_Tcoffee : GS_Tcoffee : ACCase_Tcoffee : ALS_Tcoffee : HPPD_Tcoffee : PDS_Tcoffee : PPO_Tcoffee
The sequences included in this database were collected from the USPTO Patent Full-Text Database (http://patft.uspto.gov/netahtml/PTO/index.html) and the NCBI nucleotide collection (http://www.ncbi.nlm.nih.gov/nuccore).
Some gene sequences were available in both the USPTO and NCBI databases. In these cases, the most complete sequence was included here.
Researchers interested in discovering these gene sequences from weed species not listed here may find the following tools and resources useful:
Designing degenerate primers – Instructions
A Primer for Designing Degenerate Primers http://cichlid.umd.edu/cichlidlabs/protocols/Basic/pcrdegenpri.html
Designing degenerate primers – Tools
SMS reverse translate (convert protein sequence to nucleotide sequence) http://www.bioinformatics.org/sms2/rev_trans.html
Genefisher2 (web-based program for designing degenerate primers) http://bibiserv2.cebitec.uni-bielefeld.de/genefisher2
CODEHOP (another web-based program for designing degenerate primers) http://blocks.fhcrc.org/codehop.html
HYDEN (downloadable batch program for designing degenerate primers) http://acgt.cs.tau.ac.il/hyden/
Additional Computational Links:
iPlant Collaborative: The iPlant Collaborative is a NSF-funded project that gives researchers in the plant sciences easy access to bioinformatics tools. Users can securely store terabytes of data and run this data quickly through iPlant's analysis tools and workflows without the need to go through a command-line interface. http://www.iplantcollaborative.org/
ConSurf: The ConSurf server allows users to align a set of nucleotide or protein sequences and estimate the evolutionary conservation of these residues. The conservation scores can be superimposed onto a crystal structure of the protein under investigation (if the structure is known) to visualize the protein in 3-D. http://consurf.tau.ac.il/
NCBI Blast: The NCBI Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. http://blast.ncbi.nlm.nih.gov/Blast.cgi
Disclaimer
A few entries contain only partial gene sequences or have a string of “N”s in the middle of their sequence. These “N” characters represent unknown nucleotides and are a result of sequence ambiguity at those positions. In cases where more than one allele per gene is documented per species, the most complete sequence was included. The sequences contained within this database are pulled directly from multiple public sources, including, but not limited to, GenBank, EMBL, USPTO, USPTO PSIPS, and EPO. Data from these sources have been prepared with a reasonable standard of care, but no guarantee of accuracy is made. If a more accurate sequence is available, but not currently shown on this site, please contact the database curator. Colorado State University and Monsanto lay no claim to the information provided within and all persons making use of this data are expected to adhere to the terms and conditions asserted by the authors/creators.