Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land

被引:31
作者
Romani, Facundo [1 ]
Reinheimer, Renata [2 ]
Florent, Stevie N. [3 ]
Bowman, John L. [3 ]
Moreno, Javier E. [1 ]
机构
[1] Univ Nacl Litoral, Fac Bioquim & Ciencias Biol, Ctr Cient Tecnol CONICET Santa Fe, Inst Agrobiotecnol Litoral,CONICET, Colectora Ruta Nacl 168 Km 0, RA-3000 Paraje El Pozo, Sante Fe, Argentina
[2] Univ Nacl Litoral, Fac Ciencias Agr, Ctr Cient Tecnol CONICET Santa Fe, Inst Agrobiotecnol Litoral,CONICET, Colectora Ruta Nacl 168 Km 0, RA-3000 Paraje El Pozo, Sante Fe, Argentina
[3] Monash Univ, Sch Biol Sci, Melbourne, Vic 3800, Australia
基金
澳大利亚研究理事会;
关键词
development; domain architecture; evolution; HD-Zip; land colonization; transcription factors; HD-ZIP; GENE FAMILY; DNA-BINDING; CLASS-I; ARABIDOPSIS; SEQUENCE; ORIGIN; TERRESTRIAL; PROTEIN; DOMAIN;
D O I
10.1111/nph.15133
中图分类号
Q94 [植物学];
学科分类号
071001 ;
摘要
Plant transition to land required several regulatory adaptations. The mechanisms behind these changes remain unknown. Since the evolution of transcription factors (TFs) families accompanied this transition, we studied the HOMEODOMAIN LEUCINE ZIPPER (HDZ) TF family known to control key developmental and environmental responses. We performed a phylogenetic and bioinformatics analysis of HDZ genes using transcriptomic and genomic datasets from a wide range of Viridiplantae species. We found evidence for the existence of HDZ genes in chlorophytes and early-divergent charophytes identifying several HDZ members belonging to the four known classes (I-IV). Furthermore, we inferred a progressive incorporation of auxiliary motifs. Interestingly, most of the structural features were already present in ancient lineages. Our phylogenetic analysis inferred that the origin of classes I, III, and IV is monophyletic in land plants in respect to charophytes. However, class IIHDZ genes have two conserved lineages in charophytes and mosses that differ in the CPSCE motif. Our results indicate that the HDZ family was already present in green algae. Later, the HDZ family expanded accompanying critical plant traits. Once on land, the HDZ family experienced multiple duplication events that promoted fundamental neo- and subfunctionalizations for terrestrial life.
引用
收藏
页码:408 / 421
页数:14
相关论文
共 71 条
[31]   Evolution of homeobox genes [J].
Holland, Peter W. H. .
WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY, 2013, 2 (01) :31-45
[32]   Abiotic Stress Tolerance of Charophyte Green Algae: New Challenges for Omics Techniques [J].
Holzinger, Andreas ;
Pichrtova, Martina .
FRONTIERS IN PLANT SCIENCE, 2016, 7
[33]   Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation [J].
Hori, Koichi ;
Maruyama, Fumito ;
Fujisawa, Takatomo ;
Togashi, Tomoaki ;
Yamamoto, Nozomi ;
Seo, Mitsunori ;
Sato, Syusei ;
Yamada, Takuji ;
Mori, Hiroshi ;
Tajima, Naoyuki ;
Moriyama, Takashi ;
Ikeuchi, Masahiko ;
Watanabe, Mai ;
Wada, Hajime ;
Kobayashi, Koichi ;
Saito, Masakazu ;
Masuda, Tatsuru ;
Sasaki-Sekimoto, Yuko ;
Mashiguchi, Kiyoshi ;
Awai, Koichiro ;
Shimojima, Mie ;
Masuda, Shinji ;
Iwai, Masako ;
Nobusawa, Takashi ;
Narise, Takafumi ;
Kondo, Satoshi ;
Saito, Hikaru ;
Sato, Ryoichi ;
Murakawa, Masato ;
Ihara, Yuta ;
Oshima-Yamada, Yui ;
Ohtaka, Kinuka ;
Satoh, Masanori ;
Sonobe, Kohei ;
Ishii, Midori ;
Ohtani, Ryosuke ;
Kanamori-Sato, Miyu ;
Honoki, Rina ;
Miyazaki, Daichi ;
Mochizuki, Hitoshi ;
Umetsu, Jumpei ;
Higashi, Kouichi ;
Shibata, Daisuke ;
Kamiya, Yuji ;
Sato, Naoki ;
Nakamura, Yasukazu ;
Tabata, Satoshi ;
Ida, Shigeru ;
Kurokawa, Ken ;
Ohta, Hiroyuki .
NATURE COMMUNICATIONS, 2014, 5
[34]   MRBAYES: Bayesian inference of phylogenetic trees [J].
Huelsenbeck, JP ;
Ronquist, F .
BIOINFORMATICS, 2001, 17 (08) :754-755
[35]   The impact of widespread regulatory neofunctionalization on homeolog gene evolution following whole-genome duplication in maize [J].
Hughes, Thomas E. ;
Langdale, Jane A. ;
Kelly, Steven .
GENOME RESEARCH, 2014, 24 (08) :1348-1355
[36]   PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants [J].
Jin, Jinpu ;
Tian, Feng ;
Yang, De-Chang ;
Meng, Yu-Qi ;
Kong, Lei ;
Luo, Jingchu ;
Gao, Ge .
NUCLEIC ACIDS RESEARCH, 2017, 45 (D1) :D1040-D1045
[37]   InterProScan 5: genome-scale protein function classification [J].
Jones, Philip ;
Binns, David ;
Chang, Hsin-Yu ;
Fraser, Matthew ;
Li, Weizhong ;
McAnulla, Craig ;
McWilliam, Hamish ;
Maslen, John ;
Mitchell, Alex ;
Nuka, Gift ;
Pesseat, Sebastien ;
Quinn, Antony F. ;
Sangrador-Vegas, Amaia ;
Scheremetjew, Maxim ;
Yong, Siew-Yit ;
Lopez, Rodrigo ;
Hunter, Sarah .
BIOINFORMATICS, 2014, 30 (09) :1236-1240
[38]   MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability [J].
Katoh, Kazutaka ;
Standley, Daron M. .
MOLECULAR BIOLOGY AND EVOLUTION, 2013, 30 (04) :772-780
[39]  
Kenrick P., 1997, ORIGIN EARLY DIVERSI
[40]  
Kumar S, 2016, MOL BIOL EVOL, V33, P1870, DOI [10.1093/molbev/msw054, 10.1093/molbev/msv279]