Functional & Integrative Genomics

, Volume 8, Issue 3, pp 301–307

A20/AN1 zinc-finger domain-containing proteins in plants and animals represent common elements in stress response

Authors

  • Shubha Vij
    • Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular BiologyUniversity of Delhi South Campus
    • Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular BiologyUniversity of Delhi South Campus
Short Communication

DOI: 10.1007/s10142-008-0078-7

Cite this article as:
Vij, S. & Tyagi, A.K. Funct Integr Genomics (2008) 8: 301. doi:10.1007/s10142-008-0078-7

Abstract

A20/AN1 zinc-finger domain-containing proteins are well characterized in animals, and their role in regulating the immune response is established. Recently, such A20/AN1 zinc-finger proteins have been reported from plants. These plant proteins are involved in stress response, but their exact molecular mechanism of action is yet to be deciphered. Sequence information available in public databases has been used to conduct a survey of A20/AN1 zinc-finger proteins across diverse organisms with a special emphasis on plants. Domain analysis provides some interesting insights into their biological function, the most important being that A20/AN1 zinc-finger proteins could represent common elements of stress response in plants and animals.

Keywords

A20 zinc-fingerAN1 zinc-fingerStress response

Introduction

The A20/AN1 zinc-finger domain-containing family of proteins is well characterized in animals and is known to play a central role in regulating the immune response (Huang et al. 2004; Heyninck and Beyaert 2005; Hishiya et al. 2006). The most well characterized plant A20/AN1 zinc-finger domain protein is OSISAP1 (Mukhopadhyay et al. 2004; Vij and Tyagi 2006). The gene was found to be responsive to different types of stresses including cold, desiccation, salt, submergence, heavy metals, wounding, and the stress hormone, ABA. Transgenic tobacco overexpressing OSISAP1 were found to be tolerant to cold, salt, and dehydration stress (Mukhopadhyay et al. 2004). A genome-wide analysis to identify similar genes from the complete sequence of rice and Arabidopsis (The Arabidopsis Genome Initiative 2000; International Rice Genome Sequencing Project 2005) led to the identification of 18 and 14 members, respectively, pointing to the existence of a family of such proteins in plants (Vij and Tyagi 2006). More recently, the survey was extended to Populus trichocarpa and Zea mays where 19 and 11 members containing at least the AN1 zinc-finger domain were identified, respectively (Jin et al. 2007). Expression analysis of the rice A20/AN1 zinc-finger encoding genes indicated that all the members were responsive to abiotic stress conditions (Vij and Tyagi 2006). Furthermore, the expression profile of maize and Arabidopsis genes analyzed under abiotic stress conditions using northern blot and digital northern analysis, respectively, showed the involvement of a large number of these genes in abiotic stress response (Jin et al. 2007). Thus, the plant A20/AN1 zinc-finger domain-encoding genes are associated with the plant’s response to abiotic stress.

Largely due to its polygenic nature, abiotic stress has been a complex trait to decipher (Vij and Tyagi 2007). Our knowledge of the genes involved in abiotic stress has come through conventional approaches and more lately through genome-wide expression profiling. The genes involved in abiotic stress can be broadly classified as those involved in regulation including genes involved in stress perception and signal transduction which serve to amplify the signal and notify parallel pathways to regulate the expression of the second class of proteins, the effectors which actually help the plant to mitigate stress (Vij and Tyagi 2007). The A20/AN1 zinc-finger domain proteins most probably belong to the regulatory class of proteins in the stress signaling cascade, as they lack any typical nuclear localization signal, and such proteins in animals have already been shown to function in the cytosol. The aim of the present analysis was to investigate the diversity and distribution of A20/AN1 zinc-finger domain-containing proteins across various taxa. Towards this end, A20/AN1 domain-containing proteins were searched across 22 organisms chosen in such a way so as to represent diverse taxonomic groups. Domain analysis of this class of proteins revealed diversity in architecture and in the type of domains with which the A20/AN1 zinc-finger domains were associated across protists, fungi, plants, and animals.

Materials and methods

A20/AN1 zinc-finger domain-containing protein sequences were retrieved from NCBI protein database using ‘A20 zinc-finger’ and ‘AN1 zinc-finger’ as keywords. As an alternate route, an A20/AN1 zinc-finger domain-containing protein was used for BLAST search in the NCBI protein (nr) database. The sequences retrieved in this way were BLAT searched (at 100% identity) followed by a BLAST search at >99% coverage and >99% identity to identify and remove potentially redundant sequences. SMART database (http://smart.embl-heidelberg.de/) was used for identification and retrieval of A20/AN1 zinc-finger domain-specific sequence. These sequences were aligned using ClustalX multiple alignment program (Thompson et al. 1997) and used for building an HMM model (Eddy 1998; http://hmmer.wustl.edu) for A20 and AN1 zinc-finger domains.

The eukaryotic genome projects listed in NCBI (http://www.ncbi.nlm.nih.gov/genomes/leuks.cgi) were searched to identify suitable genomes based on two main criteria: taxonomic position and sequencing status. Sequence data for Entamoeba histolytica, Tetrahymena thermophila, Trypanosoma brucei, Trichomonas vaginalis was obtained from TIGR (http://www.tigr.org); Plasmodium falciparum, Caenorhabditis elegans from Welcome Trust Sanger Institute (http://www.sanger.ac.uk); Thalassiosira pseudonana, Monosiga brevicollis, Naegleria gruberi, Nematostella vectensis, Phytophthora sojae, Chlamydomonas reinhardtii, Physcomitrella patens and Populus trichocarpa from DOE Joint Genome Institute (http://www.jgi.doe.gov); Saccharomyces cerevisiae from Stanford Genome Technology Centre (http://www-sequence.stanford.edu); Giardia lamblia from GiardiaDB (http://gmod.mbl.edu/perl/site/giardia14); Drosophila melanogaster and Homo sapiens from EMBL-EBI (http://www.ebi.ac.uk); Sorghum bicolor from DOE-JGI Community Sequencing Program (CSP; http://www.phytozome.net/sorghum); Vitis vinifera from Genoscope (http://www.genoscope.cns.fr/externe/English/Projets/Projet_ML/index.html). Arabidopsis thaliana and Oryza sativa A20/AN1 zinc-finger domain-containing proteins had been identified in a previous analysis (Vij and Tyagi 2006).

These datasets were searched for A20/AN1 zinc-finger domain-containing proteins using the HMM models built for A20 and the AN1 zinc-finger domain. The presence of A20/AN1 domains in the retrieved sequences was verified using SMART (http://smart.embl-heidelberg.de) and Interpro scan (http://www.ebi.ac.uk/interpro).

Results

Identification of A20/AN1 zinc-finger domain-containing proteins

A20/AN1 zinc-finger domain-containing proteins were identified through searches in the NCBI nonredundant (nr) protein database representing a diverse range of organisms. HMM models specific for the A20 zinc-finger and AN1 zinc-finger domains were built by aligning the sequences corresponding to the respective domains. The organisms were chosen for the identification of A20/AN1 zinc-finger domain containing proteins in such a way that they represent unique taxonomic orders. The only exceptions were plants where five representative genomes (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Sorghum bicolor, and Vitis vinifera) were considered. In addition, within a particular order, the choice of the representative organism was made based on the completeness of its sequence information to make the analysis robust. For further details on the organisms chosen, their taxonomic position, and identity, refer to Table 1 and Supplementary Table S1. Both the A20 zinc-finger and AN1 zinc-finger-based HMM models were used to search in the protein datasets available for the chosen genomes. In the case of rice and Arabidopsis, information available in our previous analysis was used (Vij and Tyagi 2006). The presence of A20/AN1 zinc-finger domains in the sequences obtained was confirmed using SMART (http://smart.embl-heidelberg.de) and Interpro scan (http://www.ebi.ac.uk/interpro).
Table 1

A20/AN1 zinc-finger domain containing proteins in various organisms

S.No.

Organism

IDa

Taxonomic group

A20/AN1 proteins

1

Plasmodium falciparum

Plfa

Apicomplexa

2

2

Thalassiosira pseudonana

Thps

Bacillariophyta

2

3

Monosiga brevicollis

Mobr

Choanoflagellida

3

4

Entamoeba histolytica

Enhi

Entamoebidae

1

5

Saccharomyces cerevisiae

Sace

Fungi

2

6

Naegleria gruberi

Nagr

Heterolobosea

10

7

Giardia lamblia

Gila

Hexamitidae

0

8

Tetrahymena thermophila

Teth

Intramacronucleata

3

9

Trypanosoma brucei

Trbr

Kinetoplastida

1

10

Drosophila melanogaster

Drme

Metazoa; Arthropoda

7

11

Homo sapiens

Hosa

Metazoa; Chordata

15

12.

Nematostella vectensis

Neve

Metazoa; Cnidaria

8

13

Caenorhabditis elegans

Cael

Metazoa; Nematoda

4

14

Phytophthora sojae

Phso

Peronosporales

3

15

Trichomonas vaginalis

Trva

Trichomonada

1

16

Chlamydomonas reinhardtii

Chre

Viridiplantae; Chlorophyta

3

17

Physcomitrella patens

Phpa

Viridiplantae; Streptophyta

10

18

Vitis vinifera

Vivi

Viridiplantae; Streptophyta

10

19

Arabidopsis thaliana

AtSAP

Viridiplantae; Streptophyta

14

20

Oryza sativa

OsSAP

Viridiplantae; Streptophyta

18

21

Sorghum bicolor

Sobi

Viridiplantae; Streptophyta

18

22

Populus trichocarpa

Potr

Viridiplantae; Streptophyta

19

aThe first two letters of genus and the first two letters of species are used to represent the identity of proteins.

The number of A20/AN1 proteins identified was 1 in Entamoeba histolytica, Trypanosoma brucei, and Trichomonas vaginalis, 2 in Plasmodium falciparum, Thalassiosira pseudonana, and Saccharomyces cerevisiae, 3 in Monosiga brevicollis, Tetrahymena thermophila, Phytophthora sojae, Chlamydomonas reinhardtii, 4 in Caenorhabditis elegans, 7 in Drosophila melanogaster, 8 in Nematostella vectensis, 10 in Naegleria gruberi, Physcomitrella patens, and Vitis vinifera, 15 in Homo sapiens, 18 in Sorghum bicolor, and 19 in Populus trichocarpa as against 14 and 18 identified previously in Arabidopsis and rice, respectively (Vij and Tyagi 2006). No A20/AN1 zinc-finger domain-containing protein was identified in G. lamblia.

Domain organization reveals a much higher diversity in animals in comparison to plants

SMART database (http://smart.embl-heidelberg.de) and Interpro scan (http://www.ebi.ac.uk/interpro) were used to study the domain organization of the A20/AN1 zinc-finger domain-containing proteins. Enatmoba (Entamoebidae), Plasmodium (Apicomplexa), Saccharomyces (Fungi), Tetrahymena (Intramacronucleata), Trypanosoma (Kinetoplastida), and Trichomonas (Trichomonada) were characterized by the presence of only the AN1 zinc-finger domain either present singly or doubly, and there was a total absence of the A20 zinc-finger domain. On the other hand, no AN1 domain was present in Thalassiosira (Bacillariophyta). Of the remaining organisms, in Naegleria (Heterolobosea), both the A20 and AN1 zinc-finger domains were present but not associated with each other. The most abundant type of domain organization (A20 zinc-finger domain at the N-terminus and AN1 zinc-finger domain at the C-terminus) is seen in all the remaining organisms used for analysis. In addition to being associated with the AN1 zinc-finger domain, the A20 zinc-finger domain was seen associated with VPS9, HdAC, WD40, and OTU domains. On the other hand, the AN1 zinc-finger domain was associated with UIM, UBQ, C2H2, AAA, and R3H domains in addition to the A20 zinc-finger.

A scrutiny of the domain organization with respect to the organisms analyzed showed that certain domain organizations were specific to particular taxonomic groups. For instance, 4 of the 17 domain organizations, i.e., ‘vii’ (OTU+A20), ‘viii’ (OTU+7A20), ‘xi’ (2AN1+2UIM) and ‘xv’ (AAA+R3H+AN1) were specific to humans (chordates). The ‘v’ (A20+HdAC), ‘vi’ (A20+7WD40), ‘xiii’ (2AN1+C2H2), ‘xvi’ (AAA+AN1) and ‘xvii’ (R3H+AN1) domain organizations were specific to Naegleria gruberi, Monosiga brevicollis, Arabidopsis thaliana, Phytophthora sojae, and Nematostella vectensis, respectively. The ‘ii’ (2A20+AN1) type of domain organization was specific to Oryza sativa and Sorghum bicolor. The association of the ubiquitin domain with AN1 (xiv) was found in nematodes as well as chordates. The ‘iv’ (A20+VPS9) domain architecture is seen in all the metazoans included in the analysis (cnidaria, nematoda, arthropoda and chordata). The ‘xii’ (2AN1+2C2H2) domain organization was largely seen in Viridiplantae (Chlamydomonas reinhardtii, Physcomitrella patens, Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Sorghum bicolor, and Vitis vinifera) with Phytophthora sojae (Peronosporales) as an exception (Table 2, Fig. 1). An interesting feature which emerged from the comparison of domain types associated with A20/AN1 zinc-finger domains in plants and animal groups included in the analysis showed that in the case of animals, a much larger number of additional domains were seen associated with the animal A20/AN1 zinc-finger proteins. These mainly included AAA, R3H, OTU, UBQ, UIM, and VPS9 in comparison to C2H2 being the only additional domain being associated with the plant A20/AN1 zinc-finger family. In addition, out of the 17 different types of domain organizations, proteins with the A20 zinc-finger domain at the N-terminus and AN1 zinc-finger domain at the C-terminus were the most abundant class especially in Viridiplantae. Thus, a basic difference was evident in the plant and animal A20/AN1 zinc-finger proteins with the animal proteins existing with a much larger diversity of domains. On the other hand, the plant counterparts seem to have overcome this limitation by expansion of one particular class of such proteins.
https://static-content.springer.com/image/art%3A10.1007%2Fs10142-008-0078-7/MediaObjects/10142_2008_78_Fig1_HTML.gif
Fig. 1

Domain organization of A20/AN1 zinc-finger containing proteins. A20/AN1 zinc-finger domain containing proteins are classified into A20 zinc-finger +AN1 zinc-finger (i), 2A20 zinc-finger +AN1 zinc-finger (ii), A20 zinc-finger (iii), A20 zinc-finger +VPS9 (Vacuolar sorting protein 9) (iv), A20 zinc-finger +HdAC (Histone deacetylase) (v), A20 zinc-finger +7WD40 (short ∼40 amino acid motifs, often terminating in a Trp-Asp (W-D) dipeptide) (vi), OTU (ovarian tumor) +A20 zinc-finger (vii), OTU (ovarian tumor) +7A20 zinc-finger (viii), AN1 zinc-finger (ix), 2AN1 zinc-finger (x), 2AN1 zinc-finger +2UIM (Ubiquitin Interacting Motif) (xi), 2AN1 zinc-finger +2C2H2 zinc-finger (xii), 2AN1 zinc-finger +C2H2 zinc-finger (xiii), UBQ (ubiquitin) +AN1 zinc-finger (xiv), AAA (ATPases associated with a variety of cellular activities) +R3H (single-stranded nucleic acids-binding) +AN1 zinc-finger (xv), AAA (ATPases associated with a variety of cellular activities) +AN1 zinc-finger (xvi), and R3H (single-stranded nucleic acids-binding) +AN1 zinc-finger (xvii) based on their domain organization. The identity and organization of each domain was established using SMART (http://smart.embl-heidelberg.de/) database and Interpro scan (http://www.ebi.ac.uk/interpro)

Table 2

Domain organization of A20/AN1 zinc-finger proteins

S.No

Domain

Protein ID

Total

i

A20+AN1

Plfa1, Mobr1, Drme1, Hosa2, Hosa3, Hosa7, Neve1, Neve3, Cael2, Phso1, Chre2, Phpa1, Phpa2, Phpa3, Phpa4, Phpa5, Phpa6, Potr1, Potr2, Potr3, Potr4, Potr5, Potr6, Potr7, Potr8, Potr9, Potr10, Potr11, Potr12, Potr13, Potr14, Potr15, Sobi1, Sobi2, Sobi3, Sobi4, Sobi5, Sobi6, Sobi7, Sobi8, Sobi9, Sobi10, Sobi11, Vivi1, Vivi2, Vivi3, Vivi4, Vivi5, Vivi6, Vivi7, OsSAP1, OsSAP2, OsSAP3, OsSAP4, OsSAP5, OsSAP6, OsSAP7, OsSAP8, OsSAP9, OsSAP10, OsSAP11, AtSAP1, AtSAP2, AtSAP3, AtSAP4, AtSAP5, AtSAP6, AtSAP7, AtSAP8, AtSAP9, AtSAP10

53

ii

2A20+AN1

OsSAP12, Sobi12, Sobi13, Sobi14

1

iii

A20

Thps1, Thps2, Nagr1, Nagr2, Nagr4, Nagr5, Hosa4, Chre1, OsSAP18

9

iv

A20+VPS9

Drme2, Hosa5, Hosa6, Neve2, Cael1

5

v

A20+HdAC

Nagr3

1

vi

A20+7WD40

Mobr2

1

vii

OTU+A20

Hosa8, Hosa9

2

viii

OTU+7A20

Hosa1

1

ix

AN1

Sace1, Sace2, Nagr10, Teth1, Teth3, Trbr1, Drme4, Drme5, Drme6, Drme7, Hosa14, Neve6, Neve7, Trva1, Phpa8, Phpa9, Phpa10, Potr17, Potr18, Potr19, Sobi15, Vivi8, OsSAP13, OsSAP14, OsSAP15, AtSAP14

24

x

2AN1

Enhi1, Plfa2, Mobr3, Nagr6, Nagr7, Nagr8, Nagr9, Teth2, Drme3, Hosa10, Hosa12, Neve4, Neve5, Cael3, Sobi16, Sobi17, Vivi9, OsSAP17, AtSAP12

16

xi

2AN1+2UIM

Hosa11

1

xii

2AN1+2C2H2

Phso2, Chre3, Phpa7, Potr16, Sobi18, Vivi10, OsSAP16, AtSAP11

6

xiii

2AN1+C2H2

AtSAP13

1

xiv

UBQ+AN1

Hosa13, Cael4

2

xv

AAA+R3H+AN1

Hosa15

1

xvi

AAA+AN1

Phso3

1

xvii

R3H+AN1

Neve8

1

  

Total

126

The identity of domains is same as given in Fig. 1.

Discussion

The human A20 protein is the most well-characterized A20 zinc-finger domain-containing protein. It is a cytoplasmic protein whose domain structure comprises of an ovarian tumor domain (OTU) at the N-terminus and seven A20 zinc-finger domains present in the C-terminus (Opipari et al. 1990; Heyninck and Beyaert 2005). A20 down-regulates the activation of NF-κB in response to TNFα, a pro-inflammatory cytokine. Its effect is mediated by its dual ubiquitin-editing function, with the OTU domain involved in de-ubiquitination and the A20 zinc-fingers involved in the ubiquitination of the TNF receptor-interacting protein (RIP) thus targeting it for proteasomal degradation (Wertz et al. 2004; Heyninck and Beyaert 2005). In addition, another class of well-studied A20/AN1 zinc-finger proteins in mammals is the one which is characterized by the presence of an A20 zinc-finger domain at the N-terminus and an AN1 zinc-finger domain at the C-terminus (Scott et al. 1998; Duan et al. 2000; Huang et al. 2004; Hishiya et al. 2006). One such well-characterized protein from humans is ZNF216. Detailed domain mapping experiments with ZNF216 have shown that its A20 zinc-finger domain interacts with RIP and IKKγ, whereas the AN1 domain interacts with TRAF6 to mediate its function (Huang et al. 2004). Furthermore, ZNF216 performs a function similar to the human A20 protein, as it is capable of inhibition of NF-κB activation (Huang et al. 2004). A similar protein has been characterized in mouse and found to function in protein degradation via the ubiquitin–proteasome system (UPS). The most well-characterized plant protein in this class is rice A20/AN1 zinc-finger domain stress associated protein 1 (OSISAP1). It has the same domain organization as the class with A20 zinc-finger at the N-terminus and AN1 zinc-finger at the C-terminus. OSISAP1 is responsive to multiple environmental stresses and confers abiotic stress tolerance when overexpressed in tobacco (Mukhopadhyay et al. 2004). In a later study, it was found that there are 18 and 14 such A20/AN1 zinc-finger domain-encoding genes in the rice and Arabidopsis genomes, respectively (Vij and Tyagi 2006). Furthermore, 11 and 19 proteins containing at least the AN1 zinc-finger domain have been identified in Zea mays and Populus trichocarpa, respectively (Jin et al. 2007). Expression profiling of the rice genes under cold, salt, and dehydration stress conditions revealed that each member of the family was up-regulated in response to one or the other abiotic stress, albeit at variable levels. Interestingly, expression analysis of the maize and Arabidopsis genes under abiotic stress conditions also showed that most of the genes showed stress-responsive expression (Vij and Tyagi 2006; Jin et al. 2007). In addition, a Capsicum A20/AN1 zinc-finger encoding gene has been deposited in the NCBI database as a cold-induced gene (GenBank Accession Number AAR83854), and it is identified as an AtSAP5 ortholog. PvPR3 from soybean has been previously reported as a gene coding for a pathogenesis-related protein not only due to sequence homology but also, as it was seen to be inducible by elicitor treatment (Sharma et al. 1992). A Chrysanthemum A20/AN1 zinc-finger class protein has also been deposited as a stress tolerance zinc-finger protein in the NCBI database (GenBank Accession Number ABI23728). Its AN1 zinc-finger domain is 100% identical to OsiSAP1. With the aim of studying the distribution and diversity of the A20/AN1 zinc-finger class of proteins, A20/AN1 zinc-finger domain-containing proteins were searched across 22 organisms. With the exception of G. lamblia, the A20/AN1 zinc-finger domain-containing proteins were identified in all other organisms used for analysis pointing to the universal existence of this class of proteins. The absence of any such domain-containing protein in G. lamblia is of evolutionary significance but can also be attributed to the fact that its genome sequence available at present is in the assembly (phase II) stage (http://www.ncbi.nlm.nih.gov/genomes/leuks.cgi; http://gmod.mbl.edu/perl/site/giardia14). The AN1/AN1+AN1 class could represent a primitive domain organization with it being the only type seen in Entamoeba histolyticaPlasmodium falciparum, Saccharomyces cerevisiae, Tetrahymena thermophila, Trypanosoma brucei, and Trichomonas vaginalis. In addition, in the majority of protists and fungi, the A20 and AN1 zinc-finger domains usually exist separately or with each other and were rarely seen associated with additional domains. In fact, even though the A20/AN1 zinc-finger domain containing proteins are present universally, a fundamental difference is evident in the domain organization between plants and animals. More specifically, very few types of organizations were shared between plants and animals such as ‘i’, ‘iii’, ‘ix’, and ‘x’ (A20+AN1, A20, AN1 and 2AN1) though the proteins representing these types were most abundant in nature. Very few domain organizations are specific to plants (ii, xii, xiii). In fact, the only additional domain identified with this class of proteins was the C2H2 domain (xii, xiii) in plants. However, in the case of animal-specific domain organizations, a much higher diversity is seen both in the types of domains and their organization. The additional domains identified in animals include VPS9, OTU, AAA, R3H, UBQ, and UIM (iv, vii, viii, xi, xiv, xv, xvii). Of these, at least three domains are related to ubiquitin signaling including OTU domain (ovarian tumor domain involved in de-ubiquitination), UBQ (present in ubiquitin and its homologs) and UIM present in proteasome subunit S5a and other ubiquitin-associated proteins (Hurley et al. 2006; http://smart.embl-heidelberg.de; http://www.ebi.ac.uk/interpro). Notably, the A20-AN1 zinc-finger class of proteins has also been shown to be involved in ubiquitin signaling with direct evidence available for the ubiquitin ligase activity of the A20 zinc-finger domain (Hishiya et al. 2006). Interestingly, though the plants lack in diversity of domains associated with the A20/AN1 zinc-finger domain containing family of proteins, they show expansion of a particular family (A20 zinc-finger domain at the N-terminus and AN1 zinc-finger domain present at the C-terminus) of proteins. In fact, lineage specific expansion (LSE) is evident only after the divergence of chlorophytes and embryophytes. However, it would have occurred before the monocot–dicot divergence ∼200 mya (Wolfe et al. 1989), as the expansion is clearly seen in the moss, Physcomitrella patens.

In conclusion, the A20/AN1 zinc-finger domain-containing proteins are known to be involved in stress response in plants and immune response in animals. In the present study, diversity and domain organization of this class of proteins was studied. Our results indicate that certain domain organizations were taxa-specific with only a few domain organizations shared between plants and animals. In addition, animals exhibit a much higher diversity of domain organization in comparison to plants. Furthermore, in the case of plants, distinct LSE was evident for one particular class of A20/AN1 proteins (A20 zinc-finger at the N-terminus and AN1 zinc-finger at the C-terminus). It has been seen that largely, the same set of domains form the structural and regulatory components of the eukaryotic crown group that includes plants, animals, fungi, and some protists. The major forces shaping the evolution of species have been creation of new domain architectures and expansion/contraction of gene families in a lineage-specific way (Lespinet et al. 2002). The plant A20-AN1 zinc-finger class of proteins is involved in abiotic stress response, and its expansion is in line with the previously observed expansion of gene families involved in stress response across diverse organisms. LSEs of such gene families are thought to contribute to the diversity needed to counter pathogen attack and respond to multiple environmental stresses.

Acknowledgements

The work is financially supported by the Department of Biotechnology, Government of India.

Supplementary material

10142_2008_78_MOESM1_ESM.xls (34 kb)
Table S1Nomenclature and corresponding database IDs of sequences used for analyses (XLS 34.5 kb)

Copyright information

© Springer-Verlag 2008