View source for Biology:TALE-likes

{{Pfam box
|image=PF03377.png
|caption=Pfam [[Sequence logo|sequence logo]] for its TALE-like entry constructed from TALE, RipTAL, and BATs. Repeat starts with the F/L; RVD is the final N/H.
|Name=TAL effector repeat
|Symbol=TAL_effector
|Pfam=PF03377
|InterPro=IPR005042
}}
'''Transcription Activator-Like Effector-Likes''' ('''TALE-likes''') are a group of bacterial [[Biology:DNA-binding protein|DNA binding proteins]] named for the first and still best-studied group, the [[Biology:TAL effector|TALEs]] of ''Xanthomonas'' bacteria. TALEs are important factors in the plant diseases caused by ''Xanthomonas'' bacteria, but are known primarily for their role in biotechnology as programmable DNA binding proteins, particularly in the context of [[Biology:Transcription activator-like effector nuclease|TALE nucleases]].  TALE-likes have additionally been found in many strains of the ''Ralstonia solanacearum'' bacterial species complex, in ''Paraburkholderia rhizoxinica'' strain HKI 454, and in two unknown marine bacteria.  Whether or not all these proteins form a single phylogenetic grouping is as yet unclear.

The unifying feature of the TALE-likes are their tandem arrays of DNA binding repeats. These repeats are, with few exceptions, 33-35 amino acids in length, and composed of two alpha-helices on either side of a flexible loop containing the DNA base binding residues and with neighbouring repeats joined by flexible linker loops.<ref>{{cite journal | vauthors = Deng D, Yan C, Wu J, Pan X, Yan N | title = Revisiting the TALE repeat | journal = Protein & Cell | volume = 5 | issue = 4 | pages = 297–306 | date = April 2014 | pmid = 24622844 | pmc = 3978159 | doi = 10.1007/s13238-014-0035-2 }}</ref> Evidence for this common structure comes in part from solved crystal structures of TALEs<ref>{{cite journal | vauthors = Deng D, Yan C, Pan X, Mahfouz M, Wang J, Zhu JK, Shi Y, Yan N | title = Structural basis for sequence-specific recognition of DNA by TAL effectors | journal = Science | volume = 335 | issue = 6069 | pages = 720–3 | date = February 2012 | pmid = 22223738 | pmc = 3586824 | doi = 10.1126/science.1215670 | bibcode = 2012Sci...335..720D }}</ref>  and a ''Burkholderia'' TALE-like (BAT),<ref name=pmid25004980>{{cite journal | vauthors = Stella S, Molina R, López-Méndez B, Juillerat A, Bertonati C, Daboussi F, Campos-Olivas R, Duchateau P, Montoya G | title = BuD, a helix-loop-helix DNA-binding domain for genome modification | journal = Acta Crystallographica. Section D, Biological Crystallography | volume = 70 | issue = Pt 7 | pages = 2042–52 | date = July 2014 | pmid = 25004980 | pmc = 4089491 | doi = 10.1107/S1399004714011183 | bibcode = 2014AcCrD..70.2042S }}</ref> but also from the conservation of the code that all TALE-likes use to recognise DNA-sequences. In fact, TALE, RipTAL, and BAT repeats can be mixed and matched to generate functional DNA-binding proteins with varying affinity.<ref>{{cite journal | vauthors = de Lange O, Schandry N, Wunderlich M, Berendzen KW, Lahaye T |title=Exploiting the sequence diversity of TALE-like repeats to vary the strength of dTALE-promoter interactions |journal=Synthetic Biology |date=January 2017 |volume=2 |issue=1 |pages=ysx004 |doi=10.1093/synbio/ysx004 |pmid=32995505 |pmc=7445789 |doi-access=free}}</ref>

== TALEs ==
[[Biology:TAL effector|TALEs]] are the first identified, best-studied and largest group within the TALE-likes. TALEs are found throughout the bacterial genus ''Xanthomonas'',<ref name=Ferreira2015>{{cite journal | vauthors = Ferreira RM, de Oliveira AC, Moreira LM, Belasque J, Gourbeyre E, Siguier P, Ferro MI, Ferro JA, Chandler M, Varani AM | title = A TALE of transposition: Tn3-like transposons play a major role in the spread of pathogenicity determinants of Xanthomonas citri and other xanthomonads | journal = mBio | volume = 6 | issue = 1 | pages = e02505-14 | date = February 2015 | pmid = 25691597 | pmc = 4337579 | doi = 10.1128/mBio.02505-14 }}</ref> comprising mostly plant pathogens. Those TALEs which have been studied have all been shown to be secreted as part of the Type III secretion system into host plant cells. Once inside the host cell they translocate to the nucleus, bind specific DNA sequences within host promoters and turn on downstream genes. Every part of this process is thought to be conserved across all TALEs. The single meaningful difference between individual TALEs, based on current understanding, is the specific DNA sequence that each TALE binds. TALEs from even closely related strains differ in the composition of repeats that make up their DNA binding domain.<ref name=PerezQunitero2015>{{cite journal | vauthors = Pérez-Quintero AL, Lamy L, Gordon JL, Escalon A, Cunnac S, Szurek B, Gagnevin L | title = QueTAL: a suite of tools to classify and compare TAL effectors functionally and phylogenetically | journal = Frontiers in Plant Science | volume = 6 | pages = 545 | date = 3 August 2015 | pmid = 26284082 | pmc = 4522561 | doi = 10.3389/fpls.2015.00545 | doi-access = free }}</ref> Repeat composition determines DNA binding preference. In particular position 13 of each repeat confers the DNA base preference of each repeat. During early research it was noted that almost all the differences between repeats of a single TALE repeat array are found in positions 12 and 13 and this finding led to the hypothesis that these residues determine base preference.<ref>{{cite journal|last1=Boch|first1=Jens|last2=Schornack|first2=Sebastian | name-list-style = vanc |title=Unraveling a 20-Year Enigma|journal=IS-MPMI Reporter|date=2010|issue=1|pages=3–4|url=http://www.ismpmi.org/members/IS-MPMI-Reporter/Documents/Archives/1001.pdf}}</ref> In fact repeat positions 12 and 13, referred to jointly as the Repeat Variable Diresidue (RVD) are commonly said to confer base specificity despite clear evidence that position 13 is the base determining residue.<ref>{{cite journal | vauthors = de Lange O, Binder A, Lahaye T | title = From dead leaf, to new life: TAL effectors as tools for synthetic biology | journal = The Plant Journal | volume = 78 | issue = 5 | pages = 753–71 | date = June 2014 | pmid = 24602153 | doi = 10.1111/tpj.12431 | doi-access = free }}</ref> In addition to the repeat domain TALEs  also possess a number of conserved features in the domains flanking the repeats. These include domains for type-III-secretion, nuclear localization and transcriptional activation. This allows TALEs to carry out their biological role as effector proteins secreted into host plant cells to activate expression of specific host genes.

===Diversity and evolution===

Whilst the RVD positions are commonly the only variable positions within a single TALE repeat array, there are more differences when comparing repeat arrays of different TALEs. The diversity of TALEs across the Xanthomonas genus is considerable, but a particularly striking finding is that the evolutionary history one arrives at by comparing repeat compositions differs from that found when comparing non-repeat sequences.<ref name=PerezQunitero2015/> Repeat arrays of TALEs are thought to evolve rapidly, with a number of recombinatorial processes suggested to shape repeat array evolution.<ref name=Ferreira2015/> Recombination of TALE repeat arrays has been demonstrated in a forced-selection experiment.<ref>{{cite journal | vauthors = Yang B, Sugio A, White FF | title = Avoidance of host recognition by alterations in the repetitive and C-terminal regions of AvrXa7, a type III effector of Xanthomonas oryzae pv. oryzae | journal = Molecular Plant-Microbe Interactions | volume = 18 | issue = 2 | pages = 142–9 | date = February 2005 | pmid = 15720083 | doi = 10.1094/MPMI-18-0142 | doi-access = free }}</ref> This evolutionary dynamism is thought to be made possible by the very high sequence identity of TALE repeats, which is a unique feature of TALEs as opposed to other TALE-likes.

===T-zero===

Another unique feature of TALEs is a set of four repeat structures at the N-terminal flank of the core repeat array. These structures, termed non-canonical or degenerate repeats have been shown to be vital for DNA binding,<ref>{{cite journal | vauthors = Gao H, Wu X, Chai J, Han Z | title = Crystal structure of a TALE protein reveals an extended N-terminal DNA binding region | journal = Cell Research | volume = 22 | issue = 12 | pages = 1716–20 | date = December 2012 | pmid = 23147789 | pmc = 3515758 | doi = 10.1038/cr.2012.156 }}</ref> though all but one do not contact DNA bases and thus make no contribution to sequence preference. The one exception is repeat -1, which encodes a fixed T-zero preference to all TALEs. This means that the target sequences of TALEs are always preceded by a thymine base. This is thought to be common to all TALEs, with the possible exception of TalC from ''Xanthomonas oryzae pv. oryzae'' strain AXO1947 ({{UniProt|G1FM79}}).<ref>{{cite journal | vauthors = Yu Y, Streubel J, Balzergue S, Champion A, Boch J, Koebnik R, Feng J, Verdier V, Szurek B | title = Colonization of rice leaf blades by an African strain of Xanthomonas oryzae pv. oryzae depends on a new TAL effector that induces the rice nodulin-3 Os11N3 gene | journal = Molecular Plant-Microbe Interactions | volume = 24 | issue = 9 | pages = 1102–13 | date = September 2011 | pmid = 21679014 | doi = 10.1094/MPMI-11-10-0254 | doi-access = free }}</ref>

== RipTALs ==
{{infobox nonhuman protein
|UniProt=Q8XYE3
|Symbol=brg11
|Name=TAL effector protein Brg11
|Organism=Ralstonia solanacearum (strain GMI1000)
}}

===Discovery and molecular properties===
It was noted in the 2002 publication of the genome of reference strain ''[[Biology:Ralstonia solanacearum|Ralstonia solanacearum]]'' GMI1000 that its genome encodes a protein similar to ''Xanthomonas'' TALEs.<ref>{{cite journal | vauthors = Salanoubat M, Genin S, Artiguenave F, Gouzy J, Mangenot S, Arlat M, Billault A, Brottier P, Camus JC, Cattolico L, Chandler M, Choisne N, Claudel-Renard C, Cunnac S, Demange N, Gaspin C, Lavie M, Moisan A, Robert C, Saurin W, Schiex T, Siguier P, Thébault P, Whalen M, Wincker P, Levy M, Weissenbach J, Boucher CA | title = Genome sequence of the plant pathogen Ralstonia solanacearum | journal = Nature | volume = 415 | issue = 6871 | pages = 497–502 | date = January 2002 | pmid = 11823852 | doi = 10.1038/415497a | doi-access = free }}</ref> Based on similar domain structure and repeat sequences it was presumed that this gene and homologs in other ''Ralstonia'' strains would encode proteins with the same molecular properties as TALEs, including sequence-specific DNA binding. In 2013 this was confirmed by two studies.<ref name= deLange2013>{{cite journal | vauthors = de Lange O, Schreiber T, Schandry N, Radeck J, Braun KH, Koszinowski J, Heuer H, Strauß A, Lahaye T | title = Breaking the DNA-binding code of Ralstonia solanacearum TAL effectors provides new possibilities to generate plant resistance genes against bacterial wilt disease | journal = The New Phytologist | volume = 199 | issue = 3 | pages = 773–86 | date = August 2013 | pmid = 23692030 | doi = 10.1111/nph.12324 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Li L, Atef A, Piatek A, Ali Z, Piatek M, Aouida M, Sharakuu A, Mahjoub A, Wang G, Khan S, Fedoroff NV, Zhu JK, Mahfouz MM | title = Characterization and DNA-binding specificities of Ralstonia TAL-like effectors | journal = Molecular Plant | volume = 6 | issue = 4 | pages = 1318–30 | date = July 2013 | pmid = 23300258 | pmc = 3716395 | doi = 10.1093/mp/sst006 }}</ref> These genes and the proteins they encode are referred to as RipTALs (Ralstonia injected protein TALE-like) in line with the standard nomenclature of Ralstonia effectors.<ref>{{cite journal | vauthors = Peeters N, Carrère S, Anisimova M, Plener L, Cazalé AC, Genin S | title = Repertoire, unified nomenclature and evolution of the Type III effector gene set in the Ralstonia solanacearum species complex | journal = BMC Genomics | volume = 14 | issue = 1 | pages = 859 | date = December 2013 | pmid = 24314259 | pmc = 3878972 | doi = 10.1186/1471-2164-14-859 | doi-access = free }}</ref> Whilst the DNA binding code of the core repeats is conserved with TALEs, RipTALs do not share the T-zero preference, instead they have a strict G-zero requirement.<ref name=deLange2013/> In addition repeats within a single RipTAL repeat array have multiple sequence differences beyond the RVD positions, unlike the near-identical repeats of TALEs.

RipTALs have been found in all four phylotypes of ''R. solanacearum'', making it an ancestral feature of this clade. Despite differences in the flanking domains, the sequences their RVDs target are highly similar.<ref name="pmid27582755">{{cite journal | vauthors = Schandry N, de Lange O, Prior P, Lahaye T | title = TALE-Like Effectors Are an Ancestral Feature of the Ralstonia solanacearum Species Complex and Converge in DNA Targeting Specificity | journal = Frontiers in Plant Science | volume = 7 | pages = 1225 | date = 17 August 2016 | pmid = 27582755 | pmc = 4987410 | doi = 10.3389/fpls.2016.01225 | doi-access = free }}</ref>

===Biological role===

Several lines of evidence support the idea that RipTALs function as effector proteins, promoting bacterial growth or disease by manipulating the expression of plant genes. They are secreted into plant cells by the [[Biology:Type three secretion system|Type III secretion system]], which is the main delivery system for effector proteins.<ref>{{cite journal | vauthors = Mukaihara T, Tamura N, Iwabuchi M | title = Genome-wide identification of a large repertoire of Ralstonia solanacearum type III effector proteins by a new functional screen | journal = Molecular Plant-Microbe Interactions | volume = 23 | issue = 3 | pages = 251–62 | date = March 2010 | pmid = 20121447 | doi = 10.1094/mpmi-23-3-0251 | doi-access = free }}</ref> They localize to the cell nucleus and are able to function as sequence-specific transcription factors in plant cells.<ref name=deLange2013/> In addition a strain lacking its RipTAL was shown to grow slower inside eggplant leaf tissue than the wild type.<ref>{{cite journal | vauthors = Macho AP, Guidot A, Barberis P, Beuzón CR, Genin S | title = A competitive index assay identifies several Ralstonia solanacearum type III effector mutant strains with reduced fitness in host plants | journal = Molecular Plant-Microbe Interactions | volume = 23 | issue = 9 | pages = 1197–205 | date = September 2010 | pmid = 20687809 | doi = 10.1094/MPMI-23-9-1197 | url = https://zenodo.org/record/853028 | doi-access = free }}</ref> Furthermore, a study based on DNA polymorphisms in ''ripTAL'' repeat domain sequences and host plants found a statistically significant connection between host plant and repeat domain variants.<ref>{{cite journal | vauthors = Heuer H, Yin YN, Xue QY, Smalla K, Guo JH | title = Repeat domain diversity of avrBs3-like genes in Ralstonia solanacearum strains and association with host preferences in the field | journal = Applied and Environmental Microbiology | volume = 73 | issue = 13 | pages = 4379–84 | date = July 2007 | pmid = 17468277 | pmc = 1932761 | doi = 10.1128/AEM.00367-07 | bibcode = 2007ApEnM..73.4379H }}</ref> This is expected if the RipTALs of different strains are adapted to target genes in specific host plants. Despite this, no target genes have been identified for any RipTAL, {{As of|2019|06|lc=y}}.

== BATs ==
{{infobox nonhuman protein
|UniProt=E5AV36
|Symbol=bat1
|Name=Burkholderia TALE-like protein 1
|Organism=Paraburkholderia rhizoxinica
}}

===Discovery===
The publication of the genome of bacterial strain ''[[Biology:Paraburkholderia rhizoxinica|Paraburkholderia rhizoxinica]]'' HKI 454, in 2011 <ref>{{cite journal | vauthors = Lackner G, Moebius N, Partida-Martinez LP, Boland S, Hertweck C | title = Evolution of an endofungal lifestyle: Deductions from the Burkholderia rhizoxinica genome | journal = BMC Genomics | volume = 12 | issue = 1 | pages = 210 | date = May 2011 | pmid = 21539752 | pmc = 3102044 | doi = 10.1186/1471-2164-12-210 | doi-access = free }}</ref> led to the discovery of a set of TALE-like genes that differed considerably in nature from the TALEs and RipTALS. The proteins encoded by these genes were studied for their DNA binding properties by two groups independently and named the Bats (Burkholderia TALE-likes; {{UniProt|E5AV36}}) or BurrH.<ref name=Batpaper2014>{{cite journal | vauthors = de Lange O, Wolf C, Dietze J, Elsaesser J, Morbitzer R, Lahaye T | title = Programmable DNA-binding proteins from Burkholderia provide a fresh perspective on the TALE-like repeat domain | journal = Nucleic Acids Research | volume = 42 | issue = 11 | pages = 7436–49 | date = June 2014 | pmid = 24792163 | pmc = 4066763 | doi = 10.1093/nar/gku329 }}</ref><ref name=Juillerat2014>{{cite journal | vauthors = Juillerat A, Bertonati C, Dubois G, Guyot V, Thomas S, Valton J, Beurdeley M, Silva GH, Daboussi F, Duchateau P | title = BurrH: a new modular DNA binding protein for genome engineering | journal = Scientific Reports | volume = 4 | pages = 3831 | date = January 2014 | pmid = 24452192 | pmc = 5379180 | doi = 10.1038/srep03831 | bibcode = 2014NatSR...4E3831J }}</ref> This research showed that the repeat units of the ''Burkholderia'' TALE-likes bind DNA with the same code as TALEs, governed by position 13 of each repeat. There are, however, a number of differences.

===Biological role===

''Burkholderia'' TALE-likes are composed almost entirely of repeats, lacking the large non-repetitive domains found flanking the repeats in TALEs and RpTALs. Those domains are key to the functions of TALEs and RipTALs allowing them to infiltrate the plant nucleus and turn on gene expression.  It is therefore currently unclear what the biological roles of ''Burkholderia'' TALE-likes are. What is clear is that they are not effector proteins secreted into plant cells to act as transcription factors, the biological role of TALEs and RipTALs. It is not unexpected that they may differ in biological roles from TALEs and RipTALs since the life style of the bacterium they derive from is very unlike that of TALE and RipTAL bearing bacteria. ''B. rhizoxinica'' is an endosymbiont, living inside a fungus, unlike ''Rhizopus microsporus'', a plant pathogen. The same fungus is also an opportunistic human pathogen in immuno-compromised patients, but whereas ''B. rhizoxinica'' is necessary for pathogenicity on plant hosts it is irrelevant to human infection.<ref>{{cite journal | vauthors = Partida-Martinez LP, Bandemer S, Rüchel R, Dannaoui E, Hertweck C | title = Lack of evidence of endosymbiotic toxin-producing bacteria in clinical Rhizopus isolates | journal = Mycoses | volume = 51 | issue = 3 | pages = 266–9 | date = May 2008 | pmid = 18399908 | doi = 10.1111/j.1439-0507.2007.01477.x | s2cid = 35688902 }}</ref>  It is unclear whether the ''Burkholderia'' TALE-likes are ever secreted either into the fungus, let alone into host plants.

===Uses in biotechnology===
As noted in the publications on ''Burkholderia'' TALE-likes there may be some advantages to using these proteins as a scaffold for programmable DNA-binding proteins to function as transcription factors or designer-nucleases, compared to TALEs.<ref name="Batpaper2014" /><ref name="Juillerat2014" /> It has been fused with a [[Biology:FokI|FokI]] nuclease analogous to [[Biology:Transcription activator-like effector nuclease|TALEN]].<ref name=pmid25004980/> Advantages include a shorter repeat size, more compact domain structure (no large non-repeat domains), greater repeat sequence diversity enabling the use of PCR on the genes encoding them and making them less vulnerable to recombinatorial repeat loss. In addition, Burkholderia TALE-likes have no T-zero requirement relaxing the constraints on DNA target selection. However, few uses of Burkholderia TALE-likes as programmable DNA binding proteins have been published, outside of the original characterization publications.

== MOrTLs ==
===Discovery===

In 2007 the results of a metagenomic sweep of the world's oceans by the [[Organization:J. Craig Venter Institute|J. Craig Venter Institute]] were made publicly available.<ref>{{cite journal | vauthors = Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W, Jaroszewski L, Cieplak P, Miller CS, Li H, Mashiyama ST, Joachimiak MP, van Belle C, Chandonia JM, Soergel DA, Zhai Y, Natarajan K, Lee S, Raphael BJ, Bafna V, Friedman R, Brenner SE, Godzik A, Eisenberg D, Dixon JE, Taylor SS, Strausberg RL, Frazier M, Venter JC | title = The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families | journal = PLOS Biology | volume = 5 | issue = 3 | pages = e16 | date = March 2007 | pmid = 17355171 | pmc = 1821046 | doi = 10.1371/journal.pbio.0050016 | doi-access = free }}</ref> The paper in 2014 on ''Burkholderia'' TALE-likes <ref name=Juillerat2014/> was also the first to report that two entries from that database resembled TALE-likes, based on sequence similarity. These were further characterized and assessed for their DNA-binding potential in 2015.<ref name=MOrTLspaper2014>{{cite journal | vauthors = de Lange O, Wolf C, Thiel P, Krüger J, Kleusch C, Kohlbacher O, Lahaye T | title = DNA-binding proteins from marine bacteria expand the known sequence diversity of TALE-like repeats | journal = Nucleic Acids Research | volume = 43 | issue = 20 | pages = 10065–80 | date = November 2015 | pmid = 26481363 | pmc = 4787788 | doi = 10.1093/nar/gkv1053 }}</ref> The repeat units encoded by these sequences were found to mediate DNA binding with base preference matching the TALE code, and judged likely to form structures nearly identical to Bat1 repeats based on [[Physics:Molecular dynamics|molecular dynamics]] simulations. The proteins encoded by these DNA sequences were therefore designated Marine Organism TALE-likes (MOrTLs) 1 and 2 ([[Biology:GenBank|GenBank]]: {{plainlink|https://www.ncbi.nlm.nih.gov/protein/ECG96325|ECG96325}}, {{plainlink|https://www.ncbi.nlm.nih.gov/protein/EBN91409|EBN91409}}).<ref name=MOrTLspaper2014/> Similar sequences found in metagenomes include {{plainlink|https://www.ncbi.nlm.nih.gov/protein/EBN19408|EBN19408}} and {{plainlink|https://www.ncbi.nlm.nih.gov/protein/ECR81667|ECR81667}}.<ref>{{cite web |title=Pfam alignment: PF03377 metagenome (auto-generated match) |url=http://pfam.xfam.org/family/PF03377/alignment/meta/format?format=pfam&alnType=meta&download=0 |accessdate=28 May 2019}}</ref>

===Evolutionary relationship to other TALE-likes===

Whilst repeats of MOrTL1 and 2 both conform structurally and functionally to the TALE-like norm, they differ considerably at the sequence level both from all other TALE-likes and from one another. It is not known whether they are truly homologous to the other TALE-likes, and thus constitute together with the TALEs, RipTALs and Bats a true [[Biology:Protein family|protein-family]]. Alternatively, they may have evolved independently. It is particularly difficult to judge the relationship to the other TALE-likes because almost nothing is known of the organisms that MOrTL1 and MOrTL2 come from. It is known only that they were found in two separate sea-water samples from the Gulf of Mexico and are likely to be bacteria based on size-exclusion before DNA sequencing.<ref name=MOrTLspaper2014/>

== Legal status ==
A patent for BATs and marine TALE-likes in protein engineering was filed in July 2012. {{As of|2019|05}}, it is currently pending in all jurisdictions.<ref>{{cite web | first1 = Claudia | last1 = Bertonati | first2 = Philippe | last2 = Duchateau | first3 = Alexandre | last3 = Juillerat | first4 = George | last4 = Silva | first5 = Julien | last5 = Valton | name-list-style = vanc |title=WO2014018601A2 New modular base-specific nucleic acid binding domains from burkholderia rhizoxinica proteins |url=https://patents.google.com/patent/WO2014018601A2 |website=Google Patents |date=24 July 2013}}</ref>

== References ==
{{Reflist}}

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[[Category:Proteins]]
[[Category:Evolution]]

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