RRGPredictor, a set-theory-based tool for predicting pathogen-associated molecular pattern receptors (PRRs) and resistance (R) proteins from plants.

Genomics
Raner José Santana Silva, Fabienne Micheli

Abstract

In plant-pathogen interactions, plant immunity through pathogen-associated molecular pattern receptors (PAMPs) and R proteins, also called pattern recognition receptors (PRRs), occurs in different ways depending on both plant and pathogen species. The use and search for a structural pattern based on the presence and absence of characteristic domains, regardless of their disposition within a sequence, could be efficient in identifying PRRs proteins. Here, we develop a method mainly based on text mining and set theory to identify PRR and R genes that classify them into 13 categories based on the presence and absence of the main domains. Analyzing 24 plant and algae genomes, we showed that the RRGPredictor was more efficient, specific and sensitive than other tools already available, and identified PRR proteins with variations in size and in domain distribution throughout the sequence. Besides an easy identification of new plant PRRs proteins, RRGPredictor provided a low computational cost.

References

Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Feb 3, 1999·Bioinformatics·K KarplusR Hughey
Feb 19, 2000·Current Opinion in Structural Biology·K S Gajiwala, S K Burley
Mar 29, 2000·Biochemical and Biophysical Research Communications·F LaurentP de Wit
Jan 17, 2003·Plant Physiology·Sylvie DinantGary A Thompson
Dec 19, 2003·Nucleic Acids Research·Alex BatemanSean R Eddy
Jul 31, 2004·Annual Review of Phytopathology·W E Durrant, X Dong
Nov 9, 2004·Bioinformatics·Johannes Söding
Mar 25, 2005·Biochemical Society Transactions·R Panstruga
Nov 22, 2005·The Plant Journal : for Cell and Molecular Biology·Sylvain La CameraThierry Heitz
Nov 17, 2006·Nature·Jonathan D G Jones, Jeffery L Dangl
Jan 26, 2007·Molecular Plant-microbe Interactions : MPMI·Bo ZhouGuo-Liang Wang
Mar 10, 2007·The Plant Journal : for Cell and Molecular Biology·Suzan H E J GabriëlsMatthieu H A J Joosten
Sep 22, 2007·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Jinling LiuGuoliang Wang
Oct 19, 2007·Current Opinion in Genetics & Development·Aaron R Friedman, Barbara J Baker
Nov 13, 2009·Nucleic Acids Research·Walter SanseverinoMaria Raffaella Ercolano
Feb 1, 2011·The Plant Cell·Bart P H J ThommaMatthieu H A J Joosten
Jun 19, 2012·Current Opinion in Plant Biology·Jacqueline Monaghan, Cyril Zipfel
Nov 20, 2012·Nucleic Acids Research·Walter SanseverinoMaria Raffaella Ercolano
Dec 12, 2012·BMC Research Notes·Walter Sanseverino, Maria Raffaella Ercolano
Jun 8, 2013·Frontiers in Plant Science·Nicolas DenancéAntonio Molina
Jan 2, 2014·Physiology and Molecular Biology of Plants : an International Journal of Functional Plant Biology·Raj Kumar Joshi, Sanghamitra Nayak
Jan 24, 2014·Bioinformatics·Philip JonesSarah Hunter
May 21, 2014·Current Opinion in Plant Biology·Zhifu HanJijie Chai
Jun 21, 2014·Trends in Immunology·Cyril Zipfel
Dec 3, 2014·Plant Science : an International Journal of Experimental Plant Biology·Shujing WuPing He
Dec 3, 2014·The New Phytologist·Johanna Acevedo-GarciaRalph Panstruga
Oct 10, 2015·Plant Signaling & Behavior·Su-Hwan KwakJohn Schiefelbein
Aug 12, 2016·Molecular Biology and Evolution·Yu ZhangBlake C Meyers
Nov 21, 2017·Nucleic Acids Research·Cristina M Osuna-CruzMaria R Ercolano
Sep 24, 2018·Plant Molecular Biology·Simrat Pal SinghBeat Keller
May 21, 2019·Plant & Cell Physiology·Richard RigoCéline Charon
Aug 16, 2019·Cell Host & Microbe·Hayden BurdettBostjan Kobe

❮ Previous
Next ❯

Citations

May 28, 2021·Trends in Plant Science·An-Yu DongGe-Fei Hao
Aug 5, 2021·Signal Transduction and Targeted Therapy·Danyang Li, Minghua Wu
Aug 29, 2021·Pathogens·Jonathan Javier Mucherino MuñozRonan Xavier Corrêa

❮ Previous
Next ❯

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.