Arabidopsis proteins harboring the AC search motif: [RK][YFW][DE][VIL][FV]X(8)[KR]X(1,3)[DE] [33].
Abstract
One strategy for improving responses and adaptation systems of plants to stress is to target molecules involved in signaling and transduction of the stimuli effected by stresses. One such molecule is adenylyl cyclase (AC) – an enzyme that catalyzes the conversion of adenosine 5′-triphosphate (ATP) to the second messenger, 3′,5′-cyclic adenosine monophosphate (cAMP). cAMP, in turn, transduces signals in response to the various biotic and abiotic stress factors. Surprisingly, as far as five decades ago, attempts to isolate ACs and/or detect cAMP from the research model plant, Arabidopsis thaliana, were inconclusive or a matter of serious debates due to the absence of appropriate techniques or advanced technologies. This chapter, therefore, herein takes the reader on a journey from the 1970s to the present day, unraveling the challenges encountered, developments made, and successes realized in efforts and attempts to identify and characterize ACs in A. thaliana. The chapter covers from the early age of unsuccessful attempts to the more recent and successful advanced technologies such as the motif search approach, omics analysis and homologous cloning. Perspectives on the direction that future knowledge-building around this important group of plant proteins are also shared.
Keywords
- Arabidopsis thaliana
- adenylyl cyclase
- plant signaling
- cAMP
- motif search
1. Introduction
In this chapter, we present part of our work that involves the identification and characterization of a special group of plant enzymes termed adenylyl cyclases (ACs) in the model plant
The chapter begins by introducing
2. A. thaliana as a model organism for plant research
3. The long journey to discover ACs and cAMP signaling in plants
3.1 Doubts and controversy on the possible existence of ACs or cAMP signaling in plants
Since the identification of cAMP in 1957 by Earl Wilbur Sutherland and TW Rall [21], wherein they studied the effect of adrenaline on the decomposition of glycogen into glucose in hepatocytes, a number of studies on ACs in animals and microorganisms have been performed [22, 23, 24]. Such studies included classification, sequencing, crystal structure analysis and functional characterization, ultimately leading to an unmasking of the catalytic mechanisms of this special group of enzymes [22, 23, 24]. However, despite all this impressive progress being made in other living organisms, the existence and/or functioning of ACs or cAMP in plants, still remained a matter of strong debate and serious controversy [25]. Firstly, because higher plants differ from other eukaryotic organisms in that they lack neurotransmitters and possess cell walls, therefore, the presence of plant cell walls would seem to compromise the believed and accepted mammalian AC/cAMP model [26]. Secondly, early studies of higher plant ACs were hampered by the fact that the proteins under study were mostly membrane-bound rather than soluble ones and therefore, their recovery and detection were somewhat very sneaky and difficult [27]. Thirdly, the attendant presence in crude biological extracts of active cyclic nucleotide phosphodiesterases, which hydrolyze cAMP also was a huge drawback [27]. Lastly, ACs represented a relatively very low proportion of plant cellular proteins for firm conclusions to be reached [27].
3.2 Hopes and continued debates
By the mid-1970s, both ACs and cAMP had been firmly established as important signaling molecules in animals and lower eukaryotes [1, 2, 28, 29]. Given this realization, it is not surprising that plant scientists continued to believe that this very same eukaryotic AC/cAMP signaling system was universal and therefore, operating in plants too [30]. Therefore, more work on plant AC/cAMP signaling continued. Nonetheless, further controversy and debates still ensued on these efforts, which perhaps can be best summarized by a concluding remark in one of the reviews of 1977, which stated as follows: “Our present knowledge, or rather ignorance, of cAMP in higher plants does not permit us to indulge in speculation on its function and thus to increase the disparity between available facts and conclusions, which are based solely on the conviction that plants, with respect to cAMP, should behave like animals or certain bacteria” [31]. As a result of this, plant scientists were therefore, strongly cautioned not to jump into conclusions even though they strongly believed that an AC/cAMP system existed in plants. The main reasons for this restraint were mostly technical. For instance, one criticism was mainly based on the fact that the reported results were merely either presumptive deductions from observed physiological effects of endogenously supplied cAMP or cAMP analogs, or that the conclusions were based solely onto insufficiently rigorous chromatographic identifications [31].
For instance, the demonstration of higher plant AC/cAMP activities had typically and traditionally been conducted through the use of either histochemical or biochemical procedures, whereby the histochemical procedures were predominantly based on the standard Wachstein-Meisel lead phosphate precipitation technique, which by that time, gave early indications of AC activity in
Even though not very conclusive, the procedures discussed above principally revealed that cAMP levels in higher plants were relatively very low compared to other organisms, e.g., <20 pmol/g fresh weight compared to >250 pmol/g wet weight in animals [30, 33]. Hence, because of the low AC activity and barely detectable amounts of cAMP as well as the questionable experimental procedures used to identify cAMP and/or AC activity, the significance of cAMP in higher plants remained strongly doubted and/or even overlooked [34]. For this reason, it has also been so difficult to discern function(s) of ACs or cAMP in plants [35]. Consequently, in 1995, Assmann even went on as far as to declare that no plant AC gene had ever been cloned and, moreover, in 2006, Linder also asserted that no AC molecule had ever been conclusively identified in higher plants [30, 36]. In general, it has therefore, been commonly argued that until a plant AC is either cloned and/or its protein sufficiently purified to allow for microsequencing and a complete enzymological characterization, the relevance and validity of the AC activity and/or cAMP signaling reported in plants would always be open to serious or rather very heated debates [30].
3.3 Leads and indications
Despite the uncertainty and controversy of the mid-1970s, surrounding the AC/cAMP signaling system in plants, the notion of its existence still continued to stay alive. Firstly, because of the fact that both cell-permeant 8-BrcAMP and stimulation of
3.4 Setting up the platform
The advent and era of high-throughput technologies (twenty-first century) eventually made it possible to assign functions to genes based on their homology, using the Basic Local Alignment Search Tool (BLAST). Apparently and according to Wong and Gehring in 2013 [42], higher plant ACs could not be identified using BLAST homology searches based on annotated ACs from prokaryotes, lower eukaryotes or animals because plant ACs are often part of complex multifunctional proteins with different domains and functions that are not conserved. Thus, BLAST searches with the known and experimentally confirmed ACs from other organisms could not return any plausible candidate(s). In addition, it was also noted that the pro-site signatures for class I and II ACs ((EYFG[SA]X(2)LWXLYK) and (YRNXW[NS]E[LIVM]RTLHFXG) respectively) are not present in the Arabidopsis proteome even if 2 mismatches were allowed [33]. Fortunately, between 2003 and 2011, six functional guanylyl cyclases (GCs) (structural analogs of ACs that convert guanosine 5′-triphosphate (GTP) to another second messenger, 3′,5′-cyclic guanosine monophosphate (cGMP)) from Arabidopsis were positively identified [43, 44, 45, 46, 47], using a 14 amino acid long search motif deduced from an alignment of conserved and functionally assigned amino acids in the catalytic center of annotated GCs from other organisms (prokaryotes, lower eukaryotes or animals) (Figure 1A) [48]. Subsequent to the success of this approach, another related 14 amino acid-long search motif was then designed to target ACs (Figure 1B) [33]. Based on this new motif, a BLAST search of the Arabidopsis genome then managed to retrieve a total of 14 hits (Table 1) as potential AC candidates [33]. This thus convincingly provided a platform for the plausible identification or discovery of ACs in
![](http://cdnintech.com/media/chapter/89187/1721201750-471109947/media/F1.png)
Figure 1.
Catalytic motifs of nucleotide cyclases (NCs). (A) Core motif of experimentally tested GCs in plants, wherein the red residue at position 1 does hydrogen bonding with the guanine base, the blue residue at position 3 confers substrate specificity, and the red residue at position 14 stabilizes the transition GTP/cGMP. The Mg2+/Mn2+-binding site is 1–3 residues downstream of position 14 (green). (B) The derived motif specific for ACs, where at position 3, the residue [CTGH] has been substituted with [DE] to allow for ATP binding [
Gene ID | Protein code | Name of protein |
---|---|---|
At1g73980 | AtTTM 1 | Triphosphate metalloenzyme 1 protein |
At1g26190 | AtTTM 2 | Triphosphate metalloenzyme 2 protein |
At2g11890 | AtTTM 3 | Triphosphate metalloenzyme 3 protein |
At3g14460 | AtLRR | Leucine-rich repeat protein |
At1g25240 | AtENTH | Epsin N-terminal homology protein |
At1g62590 | AtPPR | Pentatricopeptide repeat protein |
At1g68110 | AtClAP | Clathrin assembly protein |
At2g34780 | AtMEE | Maternal effect embryo arrest protein |
At3g02930 | AtMTA | Microtubule assembly protein |
At3g21465 | AtAC | Adenylyl cyclase protein |
At3g04220 | AtTIR-NBS-LRR | Toll interleukin-like receptor-nucleotide-binding site-leucine-rich repeat protein |
At3g18035 | AtLHL | Linker histone-like protein |
At3g28223 | AtFb | F-box protein |
At4g39756 | AtKRFb | Kelch repeat-containing F-box protein |
Table 1.
3.5 Breakthrough and achievements
Using a wide array of web-based approaches and molecular techniques, we studied all the 14 candidate proteins in Table 1 to determine if they were ACs. The methods used are detailed below.
3.5.1 Confirmation and validation of the presence of the AC motif in targeted protein candidates
Before any step was taken, it was necessary and important to first check and confirm presence of the AC motif in each of the targeted AC protein candidates. To do this, complete copy DNA (cDNA) and amino acid sequences of the targeted candidate were retrieved from The Arabidopsis Information Resource (TAIR) (https://www.arabidopsis.org/) followed by analysis of the amino acid sequence for presence of the motif [33], using the PROSITE database located within the Expert Protein Analysis System (ExPASy) proteomics server (https://www.expasy.org/). In addition, both the presence and location of the motif in each targeted candidate were also confirmed and validated by ACPred, available at http://gcpred.com/acpred/ [49]. (See example in Figure A1, Appendix A).
3.5.2 Computational analysis of the targeted protein candidates
Next, computational analysis of each of the targeted AC protein candidates was also undertaken to assess and determine the ability of its AC center to bind ATP and catalyze its subsequent conversion into cAMP. To do that, a 3-dimensional (3D) model of the targeted protein candidate was constructed by artificial intelligence using its AlphaFOLD beta version with low predicted error and very high confidence (pLDDT >90) [54]. This software uses a neural network-based model of artificial intelligence to predict protein structures from their amino acid sequences at an atomic level of accuracy. It first aligns the amino acid sequence input with sequences of known structures for pair-wise representation. The representation is then used to produce atomic coordinates for each residue, thus predicting the necessary rotation and then assembling a structured chain of amino acid residues. Its developers freely provide the source code for access to trained modelers and a script for predicting structures of novel input sequences [54]. In our case, the full-length amino acid sequence of each of the targeted protein candidates was submitted to the AlphaFOLD database followed by downloading of the model with the highest quality (based on C-scores). The downloaded model was then visualized and analyzed using UCSF ChimeraX next-generation molecular visualization program (v.1.10.1.) [55]. SeeSAR 3D (v.12.0.1) desktop modeling platform was then next used to perform docking of ATP (PubChem ID: 5957) to the AC center of the selected model via FlexX docking functionality [56, 57]. A structural alignment was then conducted by fragment assembly simulations based on iterative templates using the iterative threading assembly refinement (I-TASSER) server to match the selected model to an experimentally confirmed structure in the PDB library [56]. The model with the highest C-score was then analyzed using PyMOL (v.1.7.4.) (Schrödinger LLC, New York, USA) and ultimately adopted in the study. (See example in Figure A1, Appendix A).
3.5.3 Cloning and expression of the recombinant AC proteins
After determining that the AC center in the structural model of each of the targeted AC protein candidates was solvent-exposed, thus allowing for unimpeded substrate interactions and ultimately catalysis [57], we then went on to generate the respective protein candidate as a recombinant product so as to test it biochemically. To clone a fragment of each of the targeted AC protein candidates harboring the AC motif, total RNA was extracted from six-week-old
To express the recombinant AC protein, competent
3.5.4 Purification of the recombinant AC proteins
The resultant expressed recombinant AC protein (for each targeted AC candidate molecule) was purified by preparing a cleared cell lysate of the induced
To refold the purified denatured recombinant AC protein, the washed protein-bound resin was equilibrated with 2 ml of gradient buffer (8 M urea, 200 mM NaCl, 50 mM Tris-Cl; pH 8.0, and 20 mM β-mercaptoethanol) before the column was connected to a Bio-Logic F40 Duo-Flow chromatography system (Bio-Rad Laboratories Inc., California, USA), programmed to run a linear refolding gradient. The refolding gradient was performed by linearly diluting the 8 M gradient buffer to 0 M urea concentration with a refolding buffer (200 mM NaCl, 50 mM Tris-Cl; pH 8.0, 500 mM glucose, 0.05% (w/v) polyethylene glycol, 4 mM reduced glutathione, 0.04 mM oxidized glutathione, 100 mM non-detergent sulfobetaine, and 0.5 mM phenylmethanesulfonylfluoride (PMSF)) over 10 h at a flow rate of 0.5 ml/min. After refolding, the resultant renatured recombinant AC protein was eluted in 2 ml of elution buffer (200 mM NaCl, 50 mM Tris-Cl; pH 8.0, 250 mM imidazole, 20% (v/v) glycerol, and 0.5 mM PMSF). The eluted native protein recombinant was then de-salted and concentrated using a Spin-XUF filtration/concentration device with a molecular weight cut-off (MWCO) point of 3000 Da, in accordance with the manufacturer’s instructions (Corning Corp., New York, USA). Protein concentration was then determined by both the Bradford method [58] and an ND2000 nanodrop spectrophotometer (Thermo Scientific Inc., Massachusetts, USA) before the recombinant protein was stored at −20°C for further downstream uses. (Refer to Figure 2 below).
![](http://cdnintech.com/media/chapter/89187/1721201750-471109947/media/F2.png)
Figure 2.
Determination of the AC activity of
3.5.5 In vitro assaying of the recombinant AC proteins
The probable
3.5.6 Mass spectrometric analysis of the AC activities
To validate findings obtained by enzyme immunoassay, another additional method, tandem liquid chromatography-mass spectrometry (LC–MS/MS), was used. This method is capable of specifically and sensitively detecting cAMP levels at femtomolar concentrations. To do this, the acetylated cAMP samples from the immunoassay step were introduced into a Waters API Q-TOF Ultima mass spectrometer (Waters Microsep, Johannesburg, RSA) with a Waters Acquity UPLC at a flow rate of 180 ml/min. Separation was achieved in a Phenomenex Synergi (Torrance, CA) 4 μm Fusion-RP (250 × 2.0 mm) column when a gradient of solvent “A” (0.1% formic acid) and solvent “B” (100% acetonitrile) was applied over 18 min. During the first 7 min, the solvent composition was kept at 100% “A” followed by a linear gradient of up to 80% “B” for 3 min, and then a re-equilibration to the initial conditions. An electrospray ionization in the negative (W-) mode was used at a cone voltage of 35 V, to detect molecules and generate chromatograms. (See example in Figure A1, Appendix A).
3.5.7 Complementation testing of the recombinant AC proteins
To further confirm and validate the AC activities of the targeted and tested AC protein candidates, complementation testing was used. In this process, the
3.5.8 Phylogenetic analysis of the targeted protein candidates
Since classification of plant ACs has not yet been systematically undertaken and also considering that the relationship of plant ACs with the other currently existing six classes of ACs in animals and microorganisms is still very unclear, we assessed to determine if these plant proteins have any probable definitive groupings or clusters, particularly those ones harboring the AC search motif. In this regard therefore, full-length amino acid sequences of all plant proteins known to harbor the AC search motif were retrieved from the TAIR (https://www.arabidopsis.org/), NCBI (https://www.ncbi.nlm.nih.gov/) and Uniprot (https://www.uniprot.org/) websites, followed by construction of a phylogenetic tree through multiple sequence alignment and tree generation using Clustal Omega (ClustalO) (https://www.ebi.ac.uk/Tools/msa/clustalo/). (Refer to Figure 3).
![](http://cdnintech.com/media/chapter/89187/1721201750-471109947/media/F3.png)
Figure 3.
Phylogenetic tree and core motif analysis of all plant proteins currently known to harbor the AC search motif. Specific key amino acid residues in the core AC motif appear to be conserved in a certain pattern per group (yellow highlight), something that possibly could be exploited and used to predict and/or assign groups for any newly identified AC candidate harboring the same AC core motif. Asterisks indicate AC candidates presented herein in this chapter for publication consideration.
3.5.9 Bioinformatic analysis of the targeted protein candidates
Since in eukaryotes, it is widely accepted that proteins that are co-expressed often have related functions and linked coordinated regulatory systems [61, 62, 63, 64], we then sought to explore and gain insights into the probable biological functions of each of our targeted protein candidates. This was achieved by subjecting each protein candidate to correlation expression analysis and stimulus-specific expression analysis so as to obtain its expression partners and then infer function(s). For correlation expression analysis, The Arabidopsis co-expression tool (ACT) (http://www.arabidopsis.leeds.ac.uk) [65] was used across all available microarray experiments, using the targeted protein candidate as the driver molecule and leaving the list limit of all other molecules blank to obtain a full correlational list. In this search, the top 50 co-expressed proteins (CEG50) were mostly considered, based on the Pearson correlation coefficient as a measure of similarity between them.
For stimulus-specific expression analysis, the expression profiles of the CEG50 together with the targeted protein candidate (AC-CEG50 were initially screened over all available ATH1:22 K arrays, Affymetrix public microarray data in the Genevestigator V3 (https://www.genevestigator.com) using the stimulus and mutation tools [66]. To obtain a greater resolution of the protein expression profiles, the normalized microarray data were subsequently downloaded and analyzed for experiments that were found to induce differential expression of the proteins. The data were downloaded from the following repository sites; GEO (NCBI) (http://www.ncbi.nlm.nih.gov/geo/) [67], the NASCArrays (http://affymetrix.arabidopsis.info/narrays/experimentbrowse.pl) [68], and the TAIR-ATGenExpress (http://www.ebi.ac.uk/microarray-as/ae/). The downloaded array data were then analyzed and fold-change (log2) values for each experiment calculated. (See example in Figure A2, Appendix A).
3.5.10 Outcomes
Interestingly and overwhelmingly, our research approach managed to confirm AC activity in all of the studied 14 AC candidates as is detailed in Table 2 below. In the table, it can be seen that 6 of the candidates have already been published by our group while 3 are currently under review, again from our group. Therefore, in order to avoid duplications in this chapter, we only presented results for the last outstanding 5 candidates (Figure 2) for publication consideration.
Protein name | Gene ID | Annotated or confirmed function(s) | Publication status as AC |
---|---|---|---|
AtTTM 1 | At1g73980 | Leaf senescence [70] | Unpublished |
AtTTM 2 | At1g26190 | Pathogen resistance [71] | Unpublished |
AtTTM 3 | At2g11890 | Root development [72] | Under Review |
AtLRR | At3g14460 | Pathogen defense [73] | Published [51] |
AtENTH | At1g25240 | Endocytosis, pollen germination and pollen tube growth | Under Review |
AtPPR | At1g62590 | Chloroplast biogenesis and restoration of cytoplasmic male sterility | Published [50] |
AtClAP | At1g68110 | Endocytosis and plant defense | Published [69] |
AtMEE | At2g34780 | Embryogenesis and response to abiotic stress | Published [52] |
AtMTA | At3g02930 | Regulation of microtubule assembly and growth | Unpublished |
AtAC | At3g21465 | Response to biotic stress | Published [53] |
AtTIR-NBS-LRR | At3g04220 | Disease resistance | Unpublished |
AtLHL | At3g18035 | Regulation of developmental and reproductive processes, and response to abiotic stress | Published [74] |
AtFb | At3g28223 | Regulation of the cell cycle | Unpublished |
AtKRFb | At4g39756 | Regulation of the cell cycle | Under Review |
Table 2.
Current research status of the 14 Arabidopsis proteins harboring the AC search motif: [RK][YFW][DE][VIL][FV]X(8)[KR]X(1,3)[DE] [33].
4. Impact of our study
It is worth mentioning that our breakthrough in the identification of ACs in
Using the other methods, other scientists identified a total of 13 additional ACs of which 1 was identified through the omics analysis method and 12 through homologous cloning. ZmRPP13-LK3, which participates in the ABA-mediated resistance of
All in all, a total of 30 plant proteins are currently known to harbor the rationally designed AC search motif among which 22 have been experimentally confirmed as functional ACs while 8 are still yet to be confirmed [11, 12, 33, 50, 51, 52, 53, 69, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83]. Apparently, when this whole lot of 30 plant proteins harboring the rationally designed AC search motif was clustered together phylogenetically, using ClustalO, a total of 10 distinct groups emerged (Figure 3). Interestingly and when closely analyzed, the AC search motif in each of those 10 generated groups, tended to have a certain pattern, whereby its key catalytic residues are somewhat uniformly conserved per group, proposing that the motif could perhaps be utilized to predict and/or assign a group to any newly identified plant ACs harboring the very same motif. This is quiet tempting and persuading considering that currently, plant ACs have not yet been systematically classified as compared to animal and microorganismal ACs that have six established and well-known classes [90]. Thus, in future, the AC search motif could possibly be of vital essence to both the identification and classification of more/new plant ACs.
5. Brief discussion and self-reflection
It is evident that the advent of high-throughput technologies in the twenty-first century ultimately revolutionized science, allowing the uncovering of most of the previously obscured areas such as the identification of ACs in plants in this case. New technologies such as omics analysis, homologous cloning and motif search approach proved very useful and key in the identification of ACs in plants. For instance, of the total (31) currently confirmed ACs in plants, the omics analysis method identified 1 AC, the homologous cloning method identified 12 while the motif search approach identified 18. More so, this whole AC identification spectrum also covered a wide range of plant species (eleven to be specific), which among them are seven herbaceous plants (
Symbolically, the fact that our own research method (motif search approach) has overall identified up to 18 plant ACs, i.e., 12 in
6. Conclusion
The report given here has three very key/important messages. Firstly, it proves the strength and usefulness of the method (motif search approach) we used in our research group to search and identify ACs in
7. Future prospects and recommendations
Considering that ACs and their functions have also now been identified in a number of commercially important plants such as maize, tobacco, soybean, apple, cabbage and jujube, more work underlying the mechanisms of action of these important proteins should be pursued and interrogated. Such an approach will then help elucidate or reveal the exact functions or roles of these enzymes and/or their cAMP-linked signaling systems in plants.
Author contributions
OR conceived the idea; PC, AS-M, TD, EB, KS, GM, NM, MT and DK did the experiments. OR wrote the manuscript and PC edited it. All authors read and approved the manuscript.
Funding
The project was funded by the National Research Foundation (NRF) of South Africa (Grant Numbers: CSUR78843 & CSUR93635) and the Organization for Women in Science for the Developing World (OWSD).
Appendix A: Illustration of some of the results obtained during our process of searching and identifying ACs in A. thaliana
![](http://cdnintech.com/media/chapter/89187/1721201750-471109947/media/F4.png)
Figure A1.
(A) Amino acid sequence of AtPPR showing presence of the AC search motif in the cloned and recombinantly expressed protein fragment (inverted red triangles) [
![](http://cdnintech.com/media/chapter/89187/1721201750-471109947/media/F5.png)
Figure A2.
Heat map of AtClAP showing its correlation and differential expression patterns as an AC [
Appendix B: Cloning of the Arabidopsis proteins harboring the AC search motif
AC molecule | Gene ID | Primer set |
---|---|---|
AtTTM 1* | At1g73980 | Fwd: 5′-TCACCCAGAATAACTTTTGAAGTTAGTGTT-3′ |
Rev.: 5′-AGATGCGGATGCGGAGAATGATAAGACAGA-3′ | ||
AtTTM 2* | At1g26190 | Fwd: 5′-GGTCAAGACAGCAATGGAATTGAGTTTCAT-3′ |
Rev.: 5′-GTCATAGTCCGTTAACCGTGGATCATCAAA-3′ | ||
AtTTM 3 | At2g11890 | Fwd: 5′-GAAGTCGAAGTCAAGCTCCGTCTCCTAACC-3′ |
Rev.: 5′-AGGAAGTTTTCCTGACCGGAAAACAGCAAA-3′ | ||
AtLRR | At3g14460 | Fwd: 5′-CCAGGGGTTGGAAAGACTACCTTGACAGAG-3′ |
Rev.: 5′-TACTAATTCCTCCCTATCGAAAACATGACC-3′ | ||
AtENTH | At1g25240 | Fwd: 5′-GAATTTGGGGTCTCAAACGCGCACGACATT-3′ |
Rev.: 5′-GAAGGTAATCAAATCTGGTAACGTGTGAGT-3′ | ||
AtPPR | At1g62590 | Fwd: 5′-CGGAGCCAAATCGAGAAGATGAGGATCTCG-3′ |
Rev.: 5′-CATTTCCACCATTTGATCAACCAAAGCTAC-3′ | ||
AtClAP | At1g68110 | Fwd: 5′-GAATTCTGCAAAGGTTTCGGTGTCTCGAAC-3′ |
Rev.: 5′-GAATGTAATCAAATCTGGCATTGTATAAGT-3′ | ||
AtMEE | At2g34780 | Fwd: 5′-GCCCGGAAGGATCCAATGTCGGAGTTGGAG-3′ |
Rev.: 5′-GCGCCGGAATTCCGAGACTAATTGCGCTTC-3′ | ||
AtMTA* | At3g02930 | Fwd: 5′-ACTGATAAGAGGTCCCCCAAAGCTCCAACC-3′ |
Rev.: 5′-CAAAGCCTTCAACCGTATTAACTCTGACGA-3′ | ||
AtAC | At3g21465 | Fwd: 5′-GCTGCCAAAAGAGGAGACACAGAGTCGTTA-3′ |
Rev.: 5′-GCTAAGAAGAGCTTCATTCTTGTTTAACTC-3′ | ||
AtTIR-NBS-LRR* | At3g04220 | Fwd: 5′-GATTCTTCTTTTTTACTCGAAACTGTTGCT-3′ |
Rev.: 5′-TGGATCCACTTTGTAGAAAATGACTATCAC-3′ | ||
AtLHL | At3g18035 | Fwd: 5′-GGAAGGCCTAGGAGAGTTGTTGACCCTAGC-3′ |
Rev.: 5′-GAACAGAGCTTCTTGCATTGCCTCTGCTTC-3′ | ||
AtFb* | At3g28223 | Fwd: 5′-AACAACTATCGTGATCACCTTGTTGTATCC-3′ |
Rev.: 5′-AAGCTTGTCGGTTGGAGGCGAGGAAGGGAT-3′ | ||
AtKRFb | At4g39756 | Fwd: 5′-GGAATTCCCATGGCTACTGGTACGGAATCT-3′ |
Rev.: 5′-GACTCGAGCGTAGCAGCCAATGCGGGAGAG-3′ |
Table B1.
Primers used for amplification of the gene fragments of the Arabidopsis protein candidates harboring the AC search motif [RK][YFW][DE][VIL][FV]X(8)[KR]X(1,3)[DE] [33].
Each primer set was designed in such a way that the two annealing regions kept the AC search motif in between so that each resultant gene fragment would be containing the motif. Asterisks represent candidates presented herein in this chapter for publication.
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