Molecular Biology International

Molecular Biology International / 2016 / Article

Research Article | Open Access

Volume 2016 |Article ID 9156735 | 8 pages | https://doi.org/10.1155/2016/9156735

Analyses of Physcomitrella patens Ankyrin Repeat Proteins by Computational Approach

Academic Editor: Abdelali Hannoufa
Received07 Mar 2016
Revised18 May 2016
Accepted25 May 2016
Published27 Jun 2016

Abstract

Ankyrin (ANK) repeat containing proteins are evolutionary conserved and have functions in crucial cellular processes like cell cycle regulation and signal transduction. In this study, through an entirely in silico approach using the first release of the moss genome annotation, we found that at least 54 ANK proteins are present in P. patens. Based on their differential domain composition, the identified ANK proteins were classified into nine subfamilies. Comparative analysis of the different subfamilies of ANK proteins revealed that P. patens contains almost all the known subgroups of ANK proteins found in the other angiosperm species except for the ones having the TPR domain. Phylogenetic analysis using full length protein sequences supported the subfamily classification where the members of the same subfamily almost always clustered together. Synonymous divergence (dS) and nonsynonymous divergence (dN) ratios showed positive selection for the ANK genes of P. patens which probably helped them to attain significant functional diversity during the course of evolution. Taken together, the data provided here can provide useful insights for future functional studies of the proteins from this superfamily as well as comparative studies of ANK proteins.

1. Introduction

Ankyrin (ANK) repeats, composed of around 30–34 amino acids, are evolutionary conserved protein domains found to be involved in mediating protein-protein interactions [1]. In metazoans, the ANK repeat containing proteins has diversified functions in important processes like signal transduction, cell-cycle regulation, maintaining the integrity of cytoskeleton, transcriptional regulation, inflammatory response, development, and different types of cellular transport mechanisms [2]. Defect in ANK proteins has been found in a number of human diseases. For example, the ankyrin repeat domain 11 (ANKRD11) proteins interact with and also enhance the transcriptional activity of p53. In breast cancer cell lines, the expression level of ANKRD11 decreases compared to controls [3]. Ankyrin dysfunction has been linked with fatal human arrhythmias, such as the “ankyrin-B syndrome” in which there is an aberration of the human ankyrin-B gene (ANK2) [4].

The importance of ANK repeats can be underlined by their abundance in virtually all phyla. In photosynthetic organisms, these proteins have also been shown to be involved in a number of important physiological processes. Zhang and colleagues first reported on a light-dependent plant ANK protein which is involved in cell differentiation and development in Arabidopsis [5]. EMB506, a five-ANK repeat containing protein, has been shown to be essential for embryogenesis in Arabidopsis [6]. Another ANK protein, known as BOP1, is required for leaf morphogenesis [7]. XBAT32 and XBAT35 are linked with the regulation of ethylene biosynthesis [8, 9] and ethylene signaling [10], respectively. Several ANK proteins have been demonstrated to play role in responses to biotic and abiotic stresses in plants. The expression of rice OsBIANK1 gene, encoding proteins containing ANK repeats, is altered in pathogen infected rice-seedlings compared to that of the controls which suggests its involvement in disease resistance response [11]. Furthermore, Yan and colleagues have shown that the Arabidopsis ANK protein, AKR2, might be involved in regulating antioxidant metabolism during disease resistance and stress responses [12].

The recent advancement in genome sequencing has enabled the genome-wide identification and characterization of ANK proteins from several photosynthetic species like Arabidopsis [14], rice [15], and tomato [16]. The availability of the genome sequence of Physcomitrella patens [17] provided us with an excellent opportunity for a genome-wide analysis of this ANK family in bryophyte. Here, we report analyses of the ANK proteins of P. patens using first release of the moss genome annotation.

2. Methods

2.1. Data Retrieval and Identification of ANK Proteins

The publicly available protein sequences of P. patens were downloaded from the JGI Phytozome database (first release of the moss genome annotation) [18] and domain annotation of these proteins was done by InterProScan [19]. Then ANK proteins were screened by searching for the PF00023 domain using an in-house Perl script as described in a previous paper [20]. BLASTP was carried out with NCBI nonredundant protein database using the sequences retrieved from InterProScan as queries. After that, the candidate sequences were curated manually using available annotations in GenBank and existing literature. The molecular weights and isoelectric points were determined separately from online web server (http://www.bioinformatics.org/sms2/). Subcellular localization was predicted by the online web server of ProtComp 9.0 (http://www.softberry.com/berry.phtml?topic=protcomppl&group=help&subgroup=proloc).

2.2. Classification and Phylogenetic Analyses of the ANK Proteins

The proteins were classified into different subgroups based on the presence of additional conserved domains other than the ANK domain as described previously [15, 21]. Phylogenetic tree file was constructed by the online webserver, SATCHMO-JS [22]; and the tree was visualized by the Molecular Evolutionary Genetics Analysis (MEGA) software version 4.1 [23]. In addition, synonymous and nonsynonymous substitution pattern were determined as described previously [24].

3. Results and Discussion

Using our approach, we were able to identify a total of 54 proteins having at least one ANK repeat in P. patens (in the first released annotation of the moss genome). The identified sequences were further verified in a reiterative process through manual curation. The percentage of ANK proteins in P. patens (0.15%) is a bit lower compared to the other species from the tracheophyte lineage as listed in Figure 1(a).

The identified sequences from P. patens were designated as PpANK1, PpANK2,…,PpANK54, respectively, for analysis purpose during this study (Table 1). Figure 1(b) shows the distribution of the PpANKs according to the number of amino acids they contain within their primary sequence. The largest protein (PpANK8) had a length of 1,088 amino acids, while the shortest one (PpANK48) contained only 74 amino acids. The molecular weights (MW) and isoelectric points (PI) of the PpANK proteins deduced from their protein sequences are listed in Table 1. In addition, it was observed that these 54 PpANK proteins contained a total of 163 ANK repeats among themselves. The number of ANK repeats per protein in P. patens ranged in between 1 and 9, whereas the average number of repeats per protein was 3. The frequency of the proteins having different number of ANK repeats is shown in Figure 1(c). The highest number of repeats (9) was found in PpANK43 whereas PpANK4, PpANK18, PpANK22, PpANK33, and PpANK49 had just one ANK repeat motif each. In general, most ANK proteins have two to six repeats; and the largest known number of repeats is 34 that was found in a Giardia lamblia protein [25].


NCBI accession numberOur nomenclature# of repeatsLength (A.A.s)MW (KD)PI

XP_001770032PpANK1317618.544.02
XP_001770249PpANK2421122.889.52
XP_001771297PpANK3242547.578.63
XP_001774650PpANK4141847.157.01
XP_001775781PpANK5436440.218.24
XP_001756372PpANK6314415.34.43
XP_001756378PpANK7337641.114.48
XP_001777467PpANK821088116.868.18
XP_001779325PpANK9542545.816.71
XP_001757508PpANK10246350.677.19
XP_001782286PpANK11335038.414.15
XP_001782585PpANK12312112.86.29
XP_001759240PpANK13244048.176.19
XP_001783731PpANK14342147.497.01
XP_001784155PpANK15344249.877.19
XP_001765240PpANK16341947.137.75
XP_001765521PpANK17316718.48.75
XP_001753203PpANK181828.734.67
XP_001766044PpANK19334237.484.19
XP_001767452PpANK20241246.928.12
XP_001771908PpANK21243848.198.08
XP_001755743PpANK22129131.458.6
XP_001784959PpANK23624727.986.27
XP_001762570PpANK24543747.167.64
XP_001764006PpANK25233737.554.44
XP_001753287PpANK26334336.034.09
XP_001774971PpANK27337841.735.74
XP_001779754PpANK28423425.268.85
XP_001759321PpANK29360868.46.69
XP_001760427PpANK30237741.776.23
XP_001765151PpANK31462569.455.03
XP_001765275PpANK32435137.696.85
XP_001767776PpANK33175282.789.39
XP_001771059PpANK34445148.455.64
XP_001780358PpANK35363471.258.42
XP_001763413PpANK36447350.655.08
XP_001773791PpANK37327130.454.58
XP_001773863PpANK38210711.373.88
XP_001774458PpANK39273182.737.11
XP_001779036PpANK40272182.017.12
XP_001759158PpANK41275284.758.64
XP_001784362PpANK42341447.276.51
XP_001765211PpANK43979590.397.16
XP_001770763PpANK4461060114.98.03
XP_001765353PpANK45361267.048.35
XP_001754260PpANK46540243.177.72
XP_001771412PpANK47328532.424.04
XP_001755344PpANK482747.654.34
XP_001775223PpANK491910101.797.62
XP_001758257PpANK50338042.38.66
XP_001758416 PpANK513869.137.16
XP_001782553PpANK52311111.726.67
XP_001784176PpANK53236740.477.52
XP_001760375PpANK54313014.0310.41

The consensus ankyrin repeat sequence in P. patens, [ND]AxDKDGRT[PA]LHLAAxxGHxE[VA]-V[EK]LLLD[AH]GA[DN][VP], was generated by MEME webserver (http://meme.sdsc.edu/meme/intro.html) and visualized by Weblogo [26] as shown in Figure 2(a). The consensus ANK sequence in P. patens had a length of 33 amino acids and was conserved at the residues that are needed to retain the stacked L-shaped structure for protein-protein interaction, as mentioned by Mosavi and colleagues [27].

Based on their domain compositions, the predicted PpANK proteins were classified into nine subfamilies (Figure 2(a)). We have observed that a significant number of the PpANK proteins (21) had no other recognizable domain apart from the conserved ankyrin repeat and were classified as ANK-M. Proteins containing other known functional domains apart from the ANK domains were classified into the following subfamilies. Six proteins containing the RING finger domains were grouped as ANK-RF; three proteins containing the zinc-finger domain were designated as ANK-ZnF. BAR, PH and ArfGap domain containing proteins were grouped as ANK-BPA (3 members). The ANK-BTB subfamily (3 members) had broad-complex, tramtrack, and bric-a-brac domains. Nine of the PpANK proteins having either serine/threonine or tyrosine kinase domain were classified as ANK-PK. Three proteins having the Acetyl-CoA binding domain were classified as ACBP. Two proteins having the GPCR-chapero-1 domain were classified as ANK-GPCR. This specific subfamily containing the GPCR domain has only been reported to be found in tomato and has not been reported in model plant species like Arabidopsis and rice [16] (Figure 2(a)). The rest of the PpANK proteins that contained other domains including CHROMO, IQ, TM, and RCC1 were grouped as ANK-O. The structure of representative proteins from each subfamily is shown in Figure 2(b). There were no ANK proteins having the TPR domains (ANK-TPR) in P. patens, even though ANK proteins having these two domains are present in both Arabidopsis and rice [14, 15].

Next, we constructed a phylogenetic tree to compare between the members of different subfamilies of PpANKs. The tree file was generated from the Hidden Markov Model (HMM) based multiple sequence alignments of the sequences done by SATCHMO-JS and visualized by the Molecular Evolutionary Genetics Analysis (MEGA) software version 4.1 [23]. Interestingly, in most of the cases, members of the same subfamily were clustered together in the phylogenetic tree (Figure 2(c)).

We also analyzed the synonymous and nonsynonymous substitution patterns of the coding sequences of the genes encoding the ANK proteins in P. patens. The corresponding nucleotide sequences of the PpANK proteins were obtained from NCBI. Then we aligned the sequences using MEGA 4.1 and obtained the synonymous divergence (dS) and nonsynonymous divergence (dN) ratios. The ratio suggested positive selection for the genes of ANK superfamily of P. patens (Figure 2(d)). The codon based Z test indicated positive selection (data not shown) for most of the pairwise comparisons of the ANK genes. This further explains the fact that the ANK repeat encoding genes have acquired significant functional diversity by extensive domain shuffling or emerged multiple times independently, as a result of convergent evolution or parallel evolution or both [21].

In order to elucidate the function of a protein within a living cell, predicting the location where it resides in the cell is essential. In this study we have used ProtComp version 9.0 for predicting the subcellular localization of the PpANK proteins. The output revealed that the proteins are dispersed throughout the cells (Figure 3(a)). A large percentage (33%) of the PpANKs are located in the nucleus. Detailed information on the localization of each protein can be found in Supplementary Table  1 in Supplementary Material available online at http://dx.doi.org/10.1155/2016/9156735. We also tried to analyze if there is any relationship between the subfamilies of PpANKs with their respective subcellular localization. Interestingly, we have found that all the members of the ANK-BPA subfamily had similar localization pattern, that is, in the extracellular region (Additional File 1, Supplementary Table  1). For all the other subfamilies, we did not see any distinct pattern in their localization.

The PpANK sequences were also compared with the proteins in of NCBI nonredundant protein database which showed their homology with ANK proteins from diverse species ranging from bacteria to green algae to plants (Additional File 1, Supplementary Table  2). Not surprisingly, in many of the cases, the proteins having significant similarity with the corresponding PpANKs have functions either as protein binders or as kinases (Figure 3(b)). This further clarifies the fact that ANK proteins play significant role in protein-protein interaction and cellular signaling pathways.

4. Conclusion

This study mainly focused on the sequences ANK proteins: their classification and phylogenetic analysis by using the first release of the moss genome annotation. We are aware that newer versions of the moss genome annotation are already available in Phytozome. As such the results shown here do not provide a complete overview of the whole repertoire of P. patens ankyrin proteins. Moreover, experimental verification and wet-lab functional studies of the genes encoding these proteins are necessary to come to any definite conclusion about their biological function. Nevertheless this may serve as a useful reference for more detailed functional analyses as well as for the selection of appropriate candidate genes for further studies and genetic manipulation of P. patens ankyrin proteins.

Competing Interests

The authors declare that they have no competing interests.

Authors’ Contributions

Niaz Mahmood conceptualized the study. Both Niaz Mahmood and Nahid Tamanna analyzed and interpreted the data; and Niaz Mahmood wrote the paper. The final version of the paper is approved by both of the authors.

Supplementary Materials

Tables containing details of subcellular localization of each of the ANK proteins listed in this paper as well as their best similar homolog in other species are presented in Additional File 1.

  1. Supplementary Material

References

  1. J. Li, A. Mahajan, and M.-D. Tsai, “Ankyrin repeat: a unique motif mediating protein-protein interactions,” Biochemistry, vol. 45, no. 51, pp. 15168–15178, 2006. View at: Publisher Site | Google Scholar
  2. S. G. Sedgwick and S. J. Smerdon, “The ankyrin repeat: a diversity of interactions on a common structural framework,” Trends in Biochemical Sciences, vol. 24, no. 8, pp. 311–316, 1999. View at: Publisher Site | Google Scholar
  3. P. M. Neilsen, K. M. Cheney, C.-W. Li et al., “Identification of ANKRD11 as a p53 coactivator,” Journal of Cell Science, vol. 121, no. 21, pp. 3541–3552, 2008. View at: Publisher Site | Google Scholar
  4. S. M. Hashemi, T. J. Hund, and P. J. Mohler, “Cardiac ankyrins in health and disease,” Journal of Molecular and Cellular Cardiology, vol. 47, no. 2, pp. 203–209, 2009. View at: Publisher Site | Google Scholar
  5. H. Zhang, D. C. Scheirer, W. H. Fowle, and H. M. Goodman, “Expression of antisense or sense RNA of an ankyrin repeat-containing gene blocks chloroplast differentiation in Arabidopsis,” The Plant Cell, vol. 4, no. 12, pp. 1575–1588, 1992. View at: Publisher Site | Google Scholar
  6. S. Albert, B. Després, J. Guilleminot et al., “The EMB506 gene encodes a novel ankyrin repeat containing protein that is essential for the normal development of Arabidopsis embryos,” The Plant Journal, vol. 17, no. 2, pp. 169–179, 1999. View at: Publisher Site | Google Scholar
  7. M. H. Chan, H. J. Ji, G. N. Hong, and J. C. Fletcher, “BLADE-ON-PETIOLE1 encodes a BTB/POZ domain protein required for leaf morphogenesis in Arabidopsis thaliana,” Plant and Cell Physiology, vol. 45, no. 10, pp. 1361–1370, 2004. View at: Publisher Site | Google Scholar
  8. M. E. Prasad, A. Schofield, W. Lyzenga, H. Liu, and S. L. Stone, “Arabidopsis RING E3 ligase XBAT32 regulates lateral root production through its role in ethylene biosynthesis,” Plant Physiology, vol. 153, no. 4, pp. 1587–1596, 2010. View at: Publisher Site | Google Scholar
  9. W. J. Lyzenga, J. K. Booth, and S. L. Stone, “The Arabidopsis RING-type E3 ligase XBAT32 mediates the proteasomal degradation of the ethylene biosynthetic enzyme, 1-aminocyclopropane-1-carboxylate synthase 7,” The Plant Journal, vol. 71, no. 1, pp. 23–34, 2012. View at: Publisher Site | Google Scholar
  10. S. D. Carvalho, R. Saraiva, T. M. Maia, I. A. Abreu, and P. Duque, “XBAT35, a novel arabidopsis RING E3 ligase exhibiting dual targeting of its splice isoforms, is involved in ethylene-mediated regulation of apical hook curvature,” Molecular Plant, vol. 5, no. 6, pp. 1295–1309, 2012. View at: Publisher Site | Google Scholar
  11. X. Zhang, D. Li, H. Zhang, X. Wang, Z. Zheng, and F. Song, “Molecular characterization of rice OsBIANK1, encoding a plasma membrane-anchored ankyrin repeat protein, and its inducible expression in defense responses,” Molecular Biology Reports, vol. 37, no. 2, pp. 653–660, 2010. View at: Publisher Site | Google Scholar
  12. J. Yan, J. Wang, and H. Zhang, “An ankyrin repeat-containing protein plays a role in both disease resistance and antioxidation metabolism,” The Plant Journal, vol. 29, no. 2, pp. 193–202, 2002. View at: Publisher Site | Google Scholar
  13. A. Conesa, S. Götz, J. M. García-Gómez, J. Terol, M. Talón, and M. Robles, “Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research,” Bioinformatics, vol. 21, no. 18, pp. 3674–3676, 2005. View at: Publisher Site | Google Scholar
  14. C. Becerra, T. Jahrmann, P. Puigdomènech, and C. M. Vicient, “Ankyrin repeat-containing proteins in Arabidopsis: characterization of a novel and abundant group of genes coding ankyrin-transmembrane proteins,” Gene, vol. 340, no. 1, pp. 111–121, 2004. View at: Publisher Site | Google Scholar
  15. J. Huang, X. Zhao, H. Yu, Y. Ouyang, L. Wang, and Q. Zhang, “The ankyrin repeat gene family in rice: genome-wide identification, classification and expression profiling,” Plant Molecular Biology, vol. 71, no. 3, pp. 207–226, 2009. View at: Publisher Site | Google Scholar
  16. X. Yuan, S. Zhang, X. Qing et al., “Superfamily of ankyrin repeat proteins in tomato,” Gene, vol. 523, no. 2, pp. 126–136, 2013. View at: Publisher Site | Google Scholar
  17. S. A. Rensing, D. Lang, A. D. Zimmer et al., “The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants,” Science, vol. 319, no. 5859, pp. 64–69, 2008. View at: Publisher Site | Google Scholar
  18. D. M. Goodstein, S. Shu, R. Howson et al., “Phytozome: a comparative platform for green plant genomics,” Nucleic Acids Research, vol. 40, no. 1, pp. D1178–D1186, 2012. View at: Publisher Site | Google Scholar
  19. E. Quevillon, V. Silventoinen, S. Pillai et al., “InterProScan: protein domains identifier,” Nucleic Acids Research, vol. 33, no. 2, pp. W116–W120, 2005. View at: Publisher Site | Google Scholar
  20. N. Mahmood, M. M. Moosa, S. A. Matin, and H. Khan, “Members of Ectocarpus siliculosus F-box family are subjected to differential selective forces,” Interdisciplinary Bio Central, vol. 4, no. 1, 2012. View at: Publisher Site | Google Scholar
  21. N. Mahmood, M. M. Moosa, N. Tamanna, S. K. Sarker, R. A. Najnin, and S. S. Alam, “In silico analysis reveals the presence of a large number of Ankyrin repeat containing proteins in Ectocarpus siliculosus,” Interdisciplinary Sciences: Computational Life Sciences, vol. 4, no. 4, pp. 291–295, 2012. View at: Publisher Site | Google Scholar
  22. R. Hagopian, J. R. Davidson, R. S. Datta, B. Samad, G. R. Jarvis, and K. Sjölander, “SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction,” Nucleic Acids Research, vol. 38, no. 2, Article ID gkq298, pp. W29–W34, 2010. View at: Publisher Site | Google Scholar
  23. S. Kumar, M. Nei, J. Dudley, and K. Tamura, “MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences,” Briefings in Bioinformatics, vol. 9, no. 4, pp. 299–306, 2008. View at: Publisher Site | Google Scholar
  24. N. Mahmood and M. M. Moosa, “In silico analysis of the NBS protein family in Ectocarpus siliculosus,” Indian Journal of Biotechnology, vol. 12, no. 1, pp. 98–102, 2013. View at: Google Scholar
  25. H. G. Elmendorf, S. C. Rohrer, R. S. Khoury, R. E. Bouttenot, and T. E. Nash, “Examination of a novel head-stalk protein family in Giardia lamblia characterised by the pairing of ankyrin repeats and coiled-coil domains,” International Journal for Parasitology, vol. 35, no. 9, pp. 1001–1011, 2005. View at: Publisher Site | Google Scholar
  26. G. E. Crooks, G. Hon, J.-M. Chandonia, and S. E. Brenner, “WebLogo: a sequence logo generator,” Genome Research, vol. 14, no. 6, pp. 1188–1190, 2004. View at: Publisher Site | Google Scholar
  27. L. K. Mosavi, T. J. Cammett, D. C. Desrosiers, and Z.-Y. Peng, “The ankyrin repeat as molecular architecture for protein recognition,” Protein Science, vol. 13, no. 6, pp. 1435–1448, 2004. View at: Publisher Site | Google Scholar

Copyright © 2016 Niaz Mahmood and Nahid Tamanna. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


More related articles

767 Views | 156 Downloads | 1 Citation
 PDF  Download Citation  Citation
 Download other formatsMore
 Order printed copiesOrder

Related articles

We are committed to sharing findings related to COVID-19 as quickly and safely as possible. Any author submitting a COVID-19 paper should notify us at help@hindawi.com to ensure their research is fast-tracked and made available on a preprint server as soon as possible. We will be providing unlimited waivers of publication charges for accepted articles related to COVID-19. Sign up here as a reviewer to help fast-track new submissions.