Maize Genetics Cooperation Newsletter vol 81 2007
GRASSIUS: A first step in establishing regulatory networks in maize and other grasses
--Palaniswamy, S; Gray, J; Davuluri, R; Grotewold, E
The
increasing amount of genome sequence information in maize and other grasses
makes it possible to start building genome-wide regulatory networks. Towards
this goal, we have initiated the development of GRASSIUS, the Grass Regulatory
Information Server (http://grassius.org/). The ultimate goal of GRASSIUS is the
integration of information on transcription factors and cis-regulatory elements into regulatory motifs, the building blocks
of regulatory networks, across the grasses. Thus, GRASSIUS contains growing
databases on maize, rice, sorghum and sugarcane transcription factors
(GRASSTFDB) and promoter elements (GRASSPROMDB). As a first step towards the
generation of GRASSIUS, a uniform nomenclature system for proteins corresponding
to transcription factor was adopted, in which an organismal identifier (e.g.,
Zm) is followed by a letter code corresponding to the transcription factor
family member (e.g., MYB), followed by a number. In this way, for example, a
synonym for the C1-encoded protein
would be ZmMYB1. Transcription factors from these grasses are currently being
grouped into 43 families (Fig. 1), representing the major classes of regulatory
proteins identified in other plants (e.g., Arabidopsis,
see http://arabidopsis.med.ohio-state.edu/). GRASSIUS is expected to
significantly benefit from community input, for example through voluntary
curation contribu tions. The Grass Annotation Tool (GAT) is under
implementation, which would facilitate easy submission, curation and validation
of new and existing experimental data.
Experimental data will include plasmid clone descriptions/maps and
validated sequences from full-length cDNAs for each transcription family
member. Distribution information
for clones generated will be made available, translating into time and cost
savings for community users. Web
services provide a standard way of accessing publishing applications and data
sources over the internet, enabling mass acquisition and dissemination of
knowledge. We would be making use of existing web services (WSDbfetch, CitationExplorer) to
semi-automate the process of acquiring new data for GRASSIUS from literature
and from other existing resources and we would also be making GRASSIUS data
available as web services (Bio Moby) in a phased manner when a specific plant
module in our database is completed. The Web interface for GRASSIUS was
developed using the Java J2EE platform, and the databases were
developed using MySql. The GRASSIUS database will be constantly updated, thus
stay tuned.
Figure 1. Initial classification of regulatory proteins into 43 families.
(For color see online.)
The current release of Grass TFDB classified
into 43 families
|
ABI3VP1 |
Alfin
like (ALF) Family |
AP2-EREBP
(EREBP) Family |
|
ARF
Family |
ARID
Family |
ARR-B
(ARR) Family |
|
BBR/BPC
(BBR) Family |
bHLH
Family |
bZIP
Family |
|
CAMIA
(CAM) Family |
CCAAT-DR1
(CDR) Family |
CCAAT-HAP2
(CHP) Family |
|
CCAAT-HAP3
(HAP) Family |
CCAAT-HAP5
(CAP) Family |
CPP
Family |
|
E2F-DP
(E2F) Family |
EIL
Family |
G2-Related
(G2-R) Family |
|
GeBP
(GBP) Family |
GRAS
Family |
GRF
Family |
|
Homeobox
(HB) Family |
HRT
Family |
HSF
Family |
|
JUMONJI
(JMJ) Family |
MADS
Family |
MYB
Family |
|
MYB-related
(MYB-R) Family |
NAC
Family |
PHD
Family |
|
SBP
Family |
TCP
Family |
Trihelix
(THX) Family |
|
TUB
Family |
VOZ
Family |
WRKY
Family |
|
ZF-HD
Family |
Zinc
Finger Families |
|
|
|
C2C2-CO-like,
C2C2-Dof, |
|
|
|
C2C2-GATA,
C2C2-YABBY, |
|
|
|
C2H2,
C3H |
|
Please Note: Notes submitted to the Maize Genetics Cooperation
Newsletter may be cited only with consent of authors.