Genetic analysis of DEFECTIVE KERNEL1 loop function in three-dimensional body patterning in Physcomitrella patens

Plant Physiology

Volumn 166, Issue 2, 2014, Pages 903-919

  Demko, Viktor ^a,f   Perroud, Pierre FrançOis ^b   Johansen, Wenche ^c   Delwiche, Charles F ^d   Cooper, Endymion D ^d   Remme, P ^c   Ako, Ako Eugene ^c   Kugler, Karl G ^e   Mayer, Klaus F X ^e   Quatrano, Ralph ^b   Olsen, Odd Arne ^a,c  

^a NORWEGIAN UNIVERSITY OF LIFE SCIENCES   (Norway)

^b WASHINGTON UNIVERSITY   (United States)

^c INLAND NORWAY UNIVERSITY OF APPLIED SCIENCES   (Norway)

^d University of Maryland   (United States)

^e INSTITUTE OF EPIDEMIOLOGY   (Germany)

^f Faculty of Natural Sciences   (Slovakia)

Author keywords

[No Author keywords available]

Indexed keywords

VEGETABLE PROTEIN;

AMINO ACID SEQUENCE; BRYOPSIDA; CHEMISTRY; GENETICS; MOLECULAR GENETICS; MORPHOGENESIS; PHYSIOLOGY; PLANT GENE; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; BODY PATTERNING; BRYOPSIDA; GENES, PLANT; MOLECULAR SEQUENCE DATA; PLANT PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 84907790098     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.114.243758     Document Type: Article

References (62)

1. Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11: R106
2. Aoyama T, Hiwatashi Y, Shigyo M, Kofuji R, Kubo M, Ito M, Hasebe M (2012) AP2-type transcription factors determine stem cell identity in the moss Physcomitrella patens. Development 139: 3120-3129
3. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al, The Gene Ontology Consortium (2000) Gene ontology: tool for the unification of biology. Nat Genet 25: 25-29
4. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc 57: 289-300
5. Bernsel A, Viklund H, Hennerdal A, Elofsson A (2009) TOPCONS: consensus prediction of membrane protein topology. Nucleic Acids Res 37: W465-W468
6. Buda GJ, Barnes WJ, Fich EA, Park S, Yeats TH, Zhao L, Domozych DS, Rose JKC (2013) An ATP binding cassette transporter is required for cuticular wax deposition and desiccation tolerance in the moss Physcomitrella patens. Plant Cell 25: 4000-4013
7. Cove DJ, Perroud PF, Charron AJ, McDaniel SF, Khandelwal A, Quatrano RS (2009) The moss Physcomitrella patens: A novel model system for plant development and genomic studies. In Crotty DA, Gann A, eds, Emerging Model Organisms: A Laboratory Manual. Cold Spring Harbor Laboratory Press, New York, pp 69-104
8. Cox CJ, Li B, Foster PG, Embley TM, Civán P (2014) Conflicting phylogenies for early land plants are caused by composition biases among synonymous substitutions. Syst Biol 63: 272-279
9. Davis MJ, Sehgal MS, Ragan MA (2010) Automatic, context-specific generation of Gene Ontology slims. BMC Bioinformatics 11: 498
10. De Smet I, Beeckman T (2011) Asymmetric cell division in land plants and algae: the driving force for differentiation. Nat Rev Mol Cell Biol 12: 177-188
11. De Smet I, Voss U, Jürgens G, Beeckman T (2009) Receptor-like kinases shape the plant. Nat Cell Biol 11: 1166-1173
12. De Smet R, Adams KL, Vandepoele K, Van Montagu MC, Maere S, Van de Peer Y (2013) Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants. Proc Natl Acad Sci USA 110: 2898-2903
13. Falcon S, Gentleman R (2007) Using GOstats to test gene lists for GO term association. Bioinformatics 23: 257-258
14. Graham LE, Cook ME, Busse JS (2000) The origin of plants: body plan changes contributing to a major evolutionary radiation. Proc Natl Acad Sci USA 97: 4535-4540
15. Harrison CJ, Roeder AH, Meyerowitz EM, Langdale JA (2009) Local cues and asymmetric cell divisions underpin body plan transitions in the moss Physcomitrella patens. Curr Biol 19: 461-471
16. Johnson KL, Degnan KA, Ross Walker J, Ingram GC (2005) AtDEK1 is essential for specification of embryonic epidermal cell fate. Plant J 44: 114-127
17. Johnson KL, Faulkner C, Jeffree CE, Ingram GC (2008) The phytocalpain defective kernel 1 is a novel Arabidopsis growth regulator whose activity is regulated by proteolytic processing. Plant Cell 20: 2619-2630
18. Käll L, Krogh A, Sonnhammer EL (2004) A combined transmembrane topology and signal peptide prediction method. J Mol Biol 338: 1027-1036
19. Karol KG, McCourt RM, Cimino MT, Delwiche CF (2001) The closest living relatives of land plants. Science 294: 2351-2353
20. Kenrick P, Crane PR (1997) The origin and early evolution of plants on land. Nature 389: 33-39
21. Krogh A, Larsson B, von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305: 567-580
22. Kumar SB, Venkateshwaran K, Kundu S (2010) Alternative conformational model of a seed protein DeK1 for better understanding of structure-function relationship. J Prot Proteomics 1: 77-90
23. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25
24. Lau S, Slane D, Herud O, Kong J, Jürgens G (2012) Early embryogenesis in flowering plants: setting up the basic body pattern. Annu Rev Plant Biol 63: 483-506
25. Leliaert F, Smith DR, Moreau H, Herron MD, Verbruggen H, Delwiche CG, De Clerck O (2012) Phylogeny and molecular evolution of the green algae. Crit Rev Plant Sci 31: 1-46
26. Liang Z, Demko V, Wilson RC, Johnson KA, Ahmad R, Perroud PF, Quatrano R, Zhao S, Shalchian-Tabrizi K, Otegui MS, et al (2013) The catalytic domain CysPc of the DEK1 calpain is functionally conserved in land plants. Plant J 75: 742-754
27. Lid SE, Gruis D, Jung R, Lorentzen JA, Ananiev E, Chamberlin M, Niu X, Meeley R, Nichols S, Olsen OA (2002) The defective kernel 1 (dek1) gene required for aleurone cell development in the endosperm of maize grains encodes a membrane protein of the calpain gene superfamily. Proc Natl Acad Sci USA 99: 5460-5465
28. Lid SE, Olsen L, Nestestog R, Aukerman M, Brown RC, Lemmon B, Mucha M, Opsahl-Sorteberg HG, Olsen OA (2005) Mutation in the Arabidopisis thaliana DEK1 calpain gene perturbs endosperm and embryo development while over-expression affects organ development globally. Planta 221: 339-351
29. Ligrone R, Duckett JG, Renzaglia KS (2012) Major transitions in the evolution of early land plants: a bryological perspective. Ann Bot (Lond) 109: 851-871
30. McCarthy FM, Wang N, Magee GB, Nanduri B, Lawrence ML, Camon EB, Barrell DG, Hill DP, Dolan ME, Williams WP, et al (2006) AgBase: a functional genomics resource for agriculture. BMC Genomics 7: 229
31. Müller S, Wright AJ, Smith LG (2009) Division plane control in plants: new players in the band. Trends Cell Biol 19: 180-188
32. Murray JA, Jones A, Godin C, Traas J (2012) Systems analysis of shoot apical meristem growth and development: integrating hormonal and mechanical signaling. Plant Cell 24: 3907-3919
33. Netzer WJ, Hartl FU (1998) Protein folding in the cytosol: chaperonin-dependent and -independent mechanisms. Trends Biochem Sci 23: 68-73
34. Ono Y, Sorimachi H (2012) Calpains: an elaborate proteolytic system. Biochim Biophys Acta 1824: 224-236
35. Pao SS, Paulsen IT, Saier MH (1998) Major facilitator superfamily. Microbiol Mol Biol Rev 62: 1-34
36. Perroud PF, Cove DJ, Quatrano RS, McDaniel SF (2011) An experimental method to facilitate the identification of hybrid sporophytes in the moss Physcomitrella patens using fluorescent tagged lines. New Phytol 191: 301-306
37. Perroud PF, Demko V, Johansen W, Wilson RC, Olsen OA, Quatrano RS (2014) Defective Kernel 1 (DEK1) is required for three-dimensional growth in Physcomitrella patens. New Phytol 203: 794-804
38. Perroud PF, Quatrano RS (2006) The role of ARPC4 in tip growth and alignment of the polar axis in filaments of Physcomitrella patens. Cell Motil Cytoskeleton 63: 162-171
39. Pires ND, Dolan L (2012) Morphological evolution in land plants: new designs with old genes. Philos Trans R Soc Lond B Biol Sci 367: 508-518
40. Platt AR, Woodhall RW, George AL (2007) Improved DNA sequencing quality and efficiency using an optimized fast cycle sequencing protocol. Biotechniques 43: 58-62
41. Qiu YL, Li L, Wang B, Chen Z, Knoop V, Groth-Malonek M, Dombrovska O, Lee J, Kent L, Rest J, et al (2006) The deepest divergences in land plants inferred from phylogenomic evidence. Proc Natl Acad Sci USA 103: 15511-15516
42. Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA, Kamisugi Y, et al (2008) The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 319: 64-69
43. Rüßmann F, Stemp MJ, Mönkemeyer L, Etchells SA, Bracher A, Hartl FU (2012) Folding of large multidomain proteins by partial encapsulation in the chaperonin TRiC/CCT. Proc Natl Acad Sci USA 109: 21208-21215
44. Sakakibara K, Reisewitz P, Aoyama T, Friedrich T, Ando S, Sato Y, Tamada Y, Nishiyama T, Werr W, Murata T, et al (2014) WOX13-like genes are required for reprogramming of leaf and protoplast cells into stem cells in the moss Physcomitrella patens. Development 141: 1660-1670
45. Schaefer DG, Delacote F, Charlot F, Vrielynck N, Guyon-Debast A, Le Guin S, Neuhaus JM, Doutriaux MP, Nogué F (2010) RAD51 loss of function abolishes gene targeting and de-represses illegitimate integration in the moss Physcomitrella patens. DNA Repair (Amst) 9: 526-533
46. Schaefer DG, Zrÿd JP (1997) Efficient gene targeting in the moss Physcomitrella patens. Plant J 11: 1195-1206
47. Sørensen I, Fei Z, Andreas A, Willats WG, Domozych DS, Rose JK (2014) Stable transformation and reverse genetic analysis of Penium margaritaceum: a platform for studies of charophyte green algae, the immediate ancestors of land plants. Plant J 77: 339-351
48. Spinner L, Gadeyne A, Belcram K, Goussot M, Moison M, Duroc Y, Eeckhout D, De Winne N, Schaefer E, Van De Slijke E, et al (2013) A protein phosphatase 2A complex spatially controls plant cell division. Nat Commun 4: 1863
49. Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690
50. Tian Q, Olsen L, Sun B, Lid SE, Brown RC, Lemmon BE, Fosnes K, Gruis DF, Opsahl-Sorteberg HG, Otegui MS, et al (2007) Subcellular localization and functional domain studies of DEFECTIVE KERNEL1 in maize and Arabidopsis suggest a model for aleurone cell fate specification involving CRINKLY4 and SUPERNUMERARY ALEURONE LAYER1. Plant Cell 19: 3127-3145
51. Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111
52. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28: 511-515
53. Trouiller B, Schaefer DG, Charlot F, Nogué F (2006) MSH2 is essential for the preservation of genome integrity and prevents homeologous recombination in the moss Physcomitrella patens. Nucleic Acids Res 34: 232-242
54. Tusnády GE, Simon I (1998) Principles governing amino acid composition of integral membrane proteins: application to topology prediction. J Mol Biol 283: 489-506
55. Viklund H, Bernsel A, Skwark M, Elofsson A (2008) SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology. Bioinformatics 24: 2928-2929
56. Whelan S, Goldman N (2001) A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 18: 691-699
57. Xu B, Ohtani M, Yamaguchi M, Toyooka K, Wakazaki M, Sato M, Kubo M, Nakano Y, Sano R, Hiwatashi Y, et al (2014) Contribution of NAC transcription factors to plant adaptation to land. Science 343: 1505-1508
58. Yan N (2013) Structural advances for the major facilitator superfamily (MFS) transporters. Trends Biochem Sci 38: 151-159
59. Zadran S, Jourdi H, Rostamiani K, Qin Q, Bi X, Baudry M (2010) Brain-derived neurotrophic factor and epidermal growth factor activate neuronal m-calpain via mitogen-activated protein kinase-dependent phosphorylation. J Neurosci 30: 1086-1095
60. Zhao S, Liang Z, Demko V, Wilson R, Johansen W, Olsen OA, Shalchian-Tabrizi K (2012) Massive expansion of the calpain gene family in unicellular eukaryotes. BMC Evol Biol 12: 193
61. Zimmer A, Lang D, Richardt S, Frank W, Reski R, Rensing SA (2007) Dating the early evolution of plants: detection and molecular clock analyses of orthologs. Mol Genet Genomics 278: 393-402
62. Zimmer AD, Lang D, Buchta K, Rombauts S, Nishiyama T, Hasebe M, Van de Peer Y, Rensing SA, Reski R (2013) Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions. BMC Genomics 14: 498-518