View source for R gene

{{Short description|Genes in plant genomes}}
{{Pfam_box
| Symbol =  LRRK
| Name =  Leucine-rich repeat receptor-like protein kinase
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| OPM family=
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| Membranome family = 737
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{{Pfam_box
| Symbol =  LRRP
| Name =  Leucine-rich repeat receptor-like protein
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| Membranome family = 605
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{{Pfam_box
| Symbol = TIR-NBS-LRR
| Name =  TIR-NBS-LRR disease resistance proteins
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| Membranome family = 1343
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{{Pfam_box
| Symbol =  TIRP
| Name =  TIR domain plant proteins
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| Membranome family = 1344
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'''Resistance genes (R-Genes)''' are [[genes]] in [[plant]] [[genome]]s that convey [[plant disease resistance]] against [[pathogen]]s by producing R proteins. The main class of R-genes consist of a nucleotide binding domain (NB) and a [[Leucine-rich repeat|leucine rich repeat (LRR)]] domain(s) and are often referred to as (NB-LRR) R-genes or NLRs.<ref name="Arora-et-al-2019">{{cite journal | vauthors = Arora S, Steuernagel B, Gaurav K, Chandramohan S, Long Y, Matny O, Johnson R, Enk J, Periyannan S, Singh N, Asyraf Md Hatta M, Athiyannan N, Cheema J, Yu G, Kangara N, Ghosh S, Szabo LJ, Poland J, Bariana H, Jones JD, Bentley AR, Ayliffe M, Olson E, Xu SS, Steffenson BJ, Lagudah E, Wulff BB | display-authors = 6 | title = Resistance gene cloning from a wild crop relative by sequence capture and association genetics | journal = Nature Biotechnology | volume = 37 | issue = 2 | pages = 139–143 | date = February 2019 | pmid = 30718880 | doi = 10.1038/s41587-018-0007-9 | s2cid = 59603668 | url = http://psasir.upm.edu.my/id/eprint/81994/1/Resistance%20gene%20cloning%20.pdf }}</ref>  Generally, the NB domain binds either  [[Adenosine triphosphate|ATP]]/ADP or [[Guanosine triphosphate|GTP]]/GDP.  The LRR domain is often involved in protein-protein interactions as well as ligand binding.  NB-LRR R-genes can be further subdivided into toll interleukin 1 receptor (TIR-NB-LRR) and coiled-coil (CC-NB-LRR).<ref name=pmid22303251>{{cite journal | vauthors = Knepper C, Day B | title = From perception to activation: the molecular-genetic and biochemical landscape of disease resistance signaling in plants | journal = The Arabidopsis Book | volume = 8 | pages = e012 | year = 2010 | pmid = 22303251 | pmc = 3244959 | doi = 10.1199/tab.0124 }}</ref>
Resistance can be conveyed through a number of mechanisms including:
* The R protein interacts directly with an [[Avr gene]] ([http://prgdb.crg.eu/wiki/Avirulence_Genes Avirulence gene] {{Webarchive|url=https://web.archive.org/web/20191103223847/http://prgdb.crg.eu/wiki/Avirulence_Genes |date=2019-11-03 }})<ref name="Hafeez-et-al-2021" /> product of a pathogen (see [[gene-for-gene relationship|Gene-for-Gene relationship]]).
* The R protein guards another protein that detects degradation by an Avr gene (see [[Gene-for-gene relationship#The guard hypothesis|Guard Hypothesis]]).
* The R protein may detect a [[Pathogen-associated molecular pattern|Pathogen-Associated Molecular Pattern]] or PAMP (alternatively called MAMP  for microbe-associated molecular pattern).
* The R protein encodes [[enzyme]] that degrades a [[toxin]] produced by a pathogen.
Once the R protein has detected the presence of a pathogen, the plant can mount a defence against the pathogen. Because R genes confer resistance against specific pathogens, it is possible to transfer an R gene from one plant to another and make a plant resistant to a particular pathogen.
Many plant resistance proteins are [[single-pass transmembrane proteins]] that belong to [[Serine/threonine-specific protein kinase|receptor kinases]] and [[Toll-like receptor]]s. R genes are of large interest in [[crop breeding]], providing a large part of the immunity required by agricultural [[pathosystem]]s.<ref name="Arora-et-al-2019" />
== Background ==
Plant defense mechanisms depend on detection of fungal and bacterial pathogens. R genes protein syntheses are a way of identifying the pathogen effectors and stop their infection throughout the plant system. Molecules essential for pathogen defense are ''pattern recognition receptors'' (PRRs), ''wall associated kinase'' (WAKs), receptors with nucleotide-binding domain (NLRs) and leucine-rich repeats (LRRs). All these R proteins play roles in detecting and recognizing pathogen effectors, initiating multiple signal transductions inside the plant cell, these signals transductions will lead to different responses that will aid in pathogen destruction and prevention of further infection. These responses are:
*Production of Reactive Oxygen (ROS)
*Hypersensitive Response
*Closure of the stomata
*Production of different chemical compounds (terpenes, phenolic, tannins, alkaloids, phytoalexins)
Note that plants have various mechanisms to prevent and detect pathogenic infections, but factors such as geography, environment, genetic, and timing can affect the recognition pattern of a pathogen or can have an effect on the recognition of avirulent (avr) pathogens in plants.
==Pathogen recognition==
R genes synthesize proteins that will aid with the recognition of pathogenic effectors:
===Pattern recognition receptors (PRRs)===
This receptor is often composed of leucine-rich repeats (LRRs). LRRs have a wide range of bacterial (proteins), fungal (carbohydrates) and virulent (nucleic acids) recognition, this means that LRRs recognizes many different molecules but each LRRs usually has a very specific molecule it detects. The ability of PRRs to recognize various pathogenic components relies on a regulatory protein called brassinosteroid insensitive 1 –associated receptor kinase (BAK1). Once the pathogen has been recognized by PRRs the release of a kinase into the nucleus has been transduced triggering a transcriptional reprogramming.
===Wall associated kinase (WAKs)===
The plant cell wall is conformed of pectin and other molecules. Pectin has abundant galacturonic acids which is the compound that WAKs recognizes after a foreign invasion in the plant. Every WAKs (WAK1 & WAK2) has an N-terminal which interacts with pectin in the cell wall when pectin is being degraded to galacturonic acids by fungal enzymes.
Pathogen-associated molecular pattern (PAMPs) and damage-associated molecular pattern (DAMPs) are often identified by lectins which is a protein that binds specific carbohydrates.
===Nucleotide-binding domain and leucine-rich repeats (NLRs)===
Most R genes code for these immune receptor proteins.<ref name="Arora-et-al-2019" /> NLRs shifts its conformation from ADP state to and ATP state which allows it to send as signal transduction. The activation of NLRs is yet to be completely understood, according to current studies suggest that it is subject to multiple regulators (dimerization or oligomerization, epigenetic and transcriptional regulation, alternative splicing, and proteasome-mediated regulation)
Despite all these differences NLRs, PRRs, WAKs, effector trigger immunity (ETI) and PAMP-triggered immunity (PTI) there are certain similarities such as in the mechanism of signal transduction which includes mitogen-protein kinase (MAPK) cascades through phosphorylation which will be, calcium ion signaling.
An overall overview about the mechanical interaction about a plant defense and the ability of a pathogen to infect a plant would be for instance such a common interaction between bacterial flagellin and receptor-like kinase which triggers a basal immunity sending signals through MAP kinase cascades and transcriptional reprogramming mediated by plant WRKY transcription factors (Stephen T). Also plant resistance protein recognize bacterial effectors and programs resistance through ETI responses.
===Various other types===
The [[EDS1 family]] is a family of plant disease resistance proteins including the nominate ''enhanced disease susceptibility 1''/[[EDS1]] itself and ''phytoalexin deficient 4''/[[PAD4]]. The best studied examples of EDS1 and PAD4 are the [[Arabidopsis thaliana#EDS1 family|''Arabidopsis thaliana'' § EDS1 family]] members.<ref name="Lapin-et-al-2020">{{cite journal | vauthors = Lapin D, Bhandari DD, Parker JE | title = Origins and Immunity Networking Functions of EDS1 Family Proteins | journal = Annual Review of Phytopathology | volume = 58 | issue = 1 | pages = 253–276 | date = August 2020 | pmid = 32396762 | doi = 10.1146/annurev-phyto-010820-012840 | publisher = [[Annual Reviews (publisher)|Annual Reviews]] | s2cid = 218617308 }}</ref>
==Signal transduction==
A plant defense has two different types of immune system, the one that recognizes pathogen/microbes associated molecular patterns (PAMPs), and this is also known as PAMP-triggered immunity (PTI). Plant defense mechanism depends on immune receptors found on the plasma membrane and then the mechanism can sense the pathogen associated molecular patterns (PAMPs) and microbial associated molecular patterns (MAMPs). Detection of PAMPs triggers a physiological change in the cell activated by the pattern recognition receptors (PRRs) initiating a cascade response which through the recognition of PAMPs and MAMPs lead to the plant resistance. The other type of defense is also known as effector-triggered immunity (ETI) which is the second type of defense mediated by R-proteins by detecting photogenic effectors. ETI detects pathogenic factors and initiates a defense response. ETI is a much faster and amplified system than PTI and it develops onto the hypersensitive response (HR) leading the infected host cell to apoptosis. This does not terminate the pathogen cycle, it just slows the cycle down.
Plants have many ways of identifying symbiotic or foreign pathogens; one of these receptors causes fluctuations in the calcium ions and this fluctuation in the calcium ions. A transcription factor plays an important role in defenses against pathogenic invasion.
==Pathogen invasion==
Despite the sophiscation of plant defenses, some pathogens have evolved ways to overcome these defenses in order to infect and spread.
Pathogen elicitors are molecules that stimulate any plant defense; among these elicitors we can find two types of pathogen derived elicitors, pathogen/microbe associated molecular pattern (PAMPs/MAMPs), and also there is a second type which is produced by plants known as damage or danger associated molecular patterns (DAMPs). PTI is a way of responding against pathogen actions happening outside the cell, but a much stronger response like ETI is generated in response to effectors molecules. Once there is an induced resistance also known as priming, the plant can react faster and stronger to a pathogen attack. A known priming inducer is called β-aminobutyric acid (BABA) which is a non-protein amino acid.
Successful pathogens evolve changes in their chemical conformation in order to avoid detection by PRRs and WAKs.
Some viruses have mechanisms that allow them to avoid or suppress the RNA-mediated defense (RMD) that some viruses induce in non-transgenic plants. Further studies have shown that this suppression of the host defense has been done by HC-protease (HCPro) encoded in the Potyviral genome. It was later stablished that HCPro was a mechanism used to suppress post-transcriptional gene slicing (PTGs). Cucumber mosaic virus (CMV) uses a different protein called 2b ({{Pfam|PF03263}}) which is also a suppressor of PTGS in ''Nicotiana benthamiana''.
Even though HcPro and the 2b protein have different protein sequence specific to their own virus, both target the same instrument of defense through different mechanisms.
==Genetic engineering==
R genes are common subjects of [[molecular cloning|gene cloning]]. Every advance in techniques of [[genetic sequencing (disambiguation)|sequencing]] and [[gene delivery|transfer]] has eased this process, progressively requiring less [[linkage drag]], expense, and laboratory work over time. In the future even better results are expected from ever larger data sets, across ever larger numbers of individuals and populations, with ever greater resolution due to both more accurate sequencing and post-sequencing computational comparison between individuals.<ref name="Arora-et-al-2019" /><ref name="Hafeez-et-al-2021">{{cite journal | vauthors = Hafeez AN, Arora S, Ghosh S, Gilbert D, Bowden RL, Wulff BB | title = Creation and judicious application of a wheat resistance gene atlas | journal = Molecular Plant | volume = 14 | issue = 7 | pages = 1053–1070 | date = July 2021 | pmid = 33991673 | doi = 10.1016/j.molp.2021.05.014 | publisher = [[Cell Press]] | s2cid = 234683221 | doi-access = free | url = https://zenodo.org/records/4469514/files/Hafeez_et_al_2021_Wheat_R_gene_atlas.pdf }}</ref>
== See also ==
* [[Pattern recognition receptor]]
* [[Pathogenesis-related protein]]s, unrelated groups of diverse pathogen resistance proteins
== References ==
{{Reflist}}
== Further reading ==
{{More footnotes|article|date=December 2018}}
{{refbegin|32em}}
* {{cite journal | vauthors = Andersen EJ, Ali S, Byamukama E, Yen Y, Nepal MP | title = Disease Resistance Mechanisms in Plants | journal = Genes | volume = 9 | issue = 7 | pages = 339 | date = July 2018 | pmid = 29973557 | pmc = 6071103 | doi = 10.3390/genes9070339 | doi-access = free }}
* {{cite journal | vauthors = Su J, Yang L, Zhu Q, Wu H, He Y, Liu Y, Xu J, Jiang D, Zhang S | title = Active photosynthetic inhibition mediated by MPK3/MPK6 is critical to effector-triggered immunity | journal = PLOS Biology | volume = 16 | issue = 5 | pages = e2004122 | date = May 2018 | pmid = 29723186 | pmc = 5953503 | doi = 10.1371/journal.pbio.2004122 | doi-access = free }}
* {{cite journal | vauthors = Meng X, Xu J, He Y, Yang KY, Mordorski B, Liu Y, Zhang S | title = Phosphorylation of an ERF transcription factor by Arabidopsis MPK3/MPK6 regulates plant defense gene induction and fungal resistance | journal = The Plant Cell | volume = 25 | issue = 3 | pages = 1126–42 | date = March 2013 | pmid = 23524660 | pmc = 3634681 | doi = 10.1105/tpc.112.109074 }}
* {{cite journal | vauthors = Hahn MG | title = Microbial elicitors and their receptors in plants | journal = Annual Review of Phytopathology | volume = 34 | pages = 387–412 | year = 1996 | pmid = 15012549 | doi = 10.1146/annurev.phyto.34.1.387 }}
* {{cite journal | vauthors = Ashwin NM, Barnabas L, Ramesh Sundar A, Malathi P, Viswanathan R, Masi A, Agrawal GK, Rakwal R | title = Comparative secretome analysis of ''Colletotrichum falcatum'' identifies a cerato-platanin protein (EPL1) as a potential pathogen-associated molecular pattern (PAMP) inducing systemic resistance in sugarcane | journal = Journal of Proteomics | volume = 169 | pages = 2–20 | date = October 2017 | pmid = 28546091 | doi = 10.1016/j.jprot.2017.05.020 | hdl = 11577/3239370 | hdl-access = free }}
* {{cite journal | vauthors = Dev SS, Poornima P, Venu A | title = Molecular characterization and phylogenetic analysis of NBS-LRR-s in wild relatives of eggplant (''Solanum melongena'' L.). | journal = Indian Journal of Agricultural Research | date = April 2018 | volume = 52 | issue = 2 | pages = 167–71 |doi=10.18805/IJARe.A-4793 | doi-access = free }}
* {{cite journal | vauthors = Wu S, Shan L, He P | title = Microbial signature-triggered plant defense responses and early signaling mechanisms | journal = Plant Science | volume = 228 | pages = 118–26 | date = November 2014 | pmid = 25438792 | pmc = 4254448 | doi = 10.1016/j.plantsci.2014.03.001 }}
* {{cite journal | vauthors = Larkan NJ, Yu F, Lydiate DJ, Rimmer SR, Borhan MH | title = Single ''R'' Gene Introgression Lines for Accurate Dissection of the ''Brassica'' - ''Leptosphaeria'' Pathosystem | journal = Frontiers in Plant Science | volume = 7 | pages = 1771 | year = 2016 | pmid = 27965684 | pmc = 5124708 | doi = 10.3389/fpls.2016.01771 | doi-access = free }}
* {{cite journal | vauthors = Birkenbihl RP, Diezel C, Somssich IE | title = Arabidopsis WRKY33 is a key transcriptional regulator of hormonal and metabolic responses toward Botrytis cinerea infection | journal = Plant Physiology | volume = 159 | issue = 1 | pages = 266–85 | date = May 2012 | pmid = 22392279 | pmc = 3375964 | doi = 10.1104/pp.111.192641 | jstor = 41496262 }}
* {{cite journal | vauthors = Punja ZK |doi=10.1080/07060660109506935 |title=Genetic engineering of plants to enhance resistance to fungal pathogensa review of progress and future prospects |journal=Canadian Journal of Plant Pathology |volume=23 |issue=3 |pages=216–235 |year=2001 |bibcode=2001CaJPP..23..216P |s2cid=55728680 }}
* {{cite journal | vauthors = Łaźniewska J, Macioszek VK, Kononowicz AK |doi=10.1016/j.pmpp.2012.01.004 |title=Plant-fungus interface: The role of surface structures in plant resistance and susceptibility to pathogenic fungi |journal=Physiological and Molecular Plant Pathology |volume=78 |pages=24–30 |year=2012 }}
* {{cite journal | vauthors = Bhat RA, Miklis M, Schmelzer E, Schulze-Lefert P, Panstruga R | title = Recruitment and interaction dynamics of plant penetration resistance components in a plasma membrane microdomain | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 102 | issue = 8 | pages = 3135–40 | date = February 2005 | pmid = 15703292 | pmc = 549507 | doi = 10.1073/pnas.0500012102 | bibcode = 2005PNAS..102.3135B | doi-access = free }}
* {{cite journal | author = Arabidopsis Genome Initiative | title = Analysis of the genome sequence of the flowering plant Arabidopsis thaliana | journal = Nature | volume = 408 | issue = 6814 | pages = 796–815 | date = December 2000 | pmid = 11130711 | doi = 10.1038/35048692 | bibcode = 2000Natur.408..796T | doi-access = free | url = https://publications.goettingen-research-online.de/bitstream/2/110486/1/document.pdf }}
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[[Category:Plant genes]]