Systems biology for enhanced plant nitrogen nutrition.
ABSTRACT Nitrogen (N)-based fertilizers increase agricultural productivity but have detrimental effects on the environment and human health. Research is generating improved understanding of the signaling components plants use to sense N and regulate metabolism, physiology, and growth and development. However, we still need to integrate these regulatory factors into signal transduction pathways and connect them to downstream response pathways. Systems biology approaches facilitate identification of new components and N-regulatory networks linked to other plant processes. A holistic view of plant N nutrition should open avenues to translate this knowledge into effective strategies to improve N-use efficiency and enhance crop production systems for more sustainable agricultural practices.
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ABSTRACT: To identify the key elements controlling grain production in maize, it is essential to have an integrated view of the responses to alterations in the main steps of nitrogen assimilation by modification of gene expression. Two maize mutant lines (gln1.3 and gln1.4), deficient in two genes encoding cytosolic glutamine synthetase, a key enzyme involved in nitrogen assimilation, were previously characterized by a reduction of kernel size in the gln1.4 mutant and by a reduction of kernel number in the gln1.3 mutant. In this work, the differences in leaf gene transcripts, proteins and metabolite accumulation in gln1.3 and gln1.4 mutants were studied at two key stages of plant development, in order to identify putative candidate genes, proteins and metabolic pathways contributing on one hand to the control of plant development and on the other to grain production. The most interesting finding in this study is that a number of key plant processes were altered in the gln1.3 and gln1.4 mutants, including a number of major biological processes such as carbon metabolism and transport, cell wall metabolism, and several metabolic pathways and stress responsive and regulatory elements. We also found that the two mutants share common or specific characteristics across at least two or even three of the "omics" considered at the vegetative stage of plant development, or during the grain filling period. This is the first comprehensive molecular and physiological characterization of two cytosolic glutamine synthetase maize mutants using a combined transcriptomic, proteomic and metabolomic approach. We find that the integration of the three "omics" procedures is not straight forward, since developmental and mutant-specific levels of regulation seem to occur from gene expression to metabolite accumulation. However, their potential use is discussed with a view to improving our understanding of nitrogen assimilation and partitioning and its impact on grain production.BMC Genomics 11/2014; 15(1):1005. · 4.04 Impact Factor
Dataset: J. Exp. Bot.-2014-Simons-jxb eru227
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ABSTRACT: Models are used to represent aspects of the real world for specific purposes, and mathematical models have opened up new approaches in studying the behavior and complexity of biological systems. However, modeling is often time-consuming and requires significant computational resources for data development, data analysis, and simulation. Computational modeling has been successfully applied as an aid for metabolic engineering in microorganisms. But such model-based approaches have only recently been extended to plant metabolic engineering, mainly due to greater pathway complexity in plants and their highly compartmentalized cellular structure. Recent progress in plant systems biology and bioinformatics has begun to disentangle this complexity and facilitate the creation of efficient plant metabolic models. This review highlights several aspects of plant metabolic modeling in the context of understanding, predicting and modifying complex plant metabolism. We discuss opportunities for engineering photosynthetic carbon metabolism, sucrose synthesis, and the tricarboxylic acid cycle in leaves and oil synthesis in seeds and the application of metabolic modeling to the study of plant acclimation to the environment. The aim of the review is to offer a current perspective for plant biologists without requiring specialized knowledge of bioinformatics or systems biology.The Plant Cell 10/2014; · 9.58 Impact Factor
, 1673 (2012);
Rodrigo A. Gutiérrez
Systems Biology for Enhanced Plant Nitrogen Nutrition
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Systems Biology for Enhanced Plant
Rodrigo A. Gutiérrez
Nitrogen (N)–based fertilizers increase agricultural productivity but have detrimental effects on
the environment and human health. Research is generating improved understanding of the signaling
components plants use to sense N and regulate metabolism, physiology, and growth and development.
them to downstream response pathways. Systems biology approaches facilitate identification of new
should open avenues to translate this knowledge into effective strategies to improve N-use efficiency
and enhance crop production systems for more sustainable agricultural practices.
growth and development (2), crop yield (3), and
primary production at a planetary scale (4). Biolog-
are in short supply in natural as well as agricultural
systems. Consequently, N removed from the soil in
crop products or by leaching must be replaced if
agriculturalproductivityis tobe sustained.Synthetic
of ~120 Tg year−1of N used for food production
globally, only ~10% is consumed by people (5).
is lost by leaching into the soil or is released to the
cancauseeutrophication ofterrestrial and aquatic
systems, dramatically exemplified by dead zones
such as the one found in the northern Gulf of
be transformed into different chemical forms in the
environment, leading to diverse effects (4). In addi-
tion to negative environmental effects, excess nitro-
gen may also have direct negative consequences for
regarding the contribution of nitrate and nitrite to
human nutrition, physiology, and pathology.
in the greatest amount by plants (1), and
its availability, or lack thereof, limits plant
N Perception, Signaling, and Responses
In addition to their role as nutrients, nitrate and
other forms of N can act as signals to regulate
growth and development [reviewed in (11, 12)].
Nitrate is sensed by NITRATE TRANSPORTER
affinity based on the phosphorylation of threonine-
101 (T101) (13) (Fig. 1). Under low-nitrate condi-
23 (CIPK23) can phosphorylate T101, making
a weak induction of gene expression of NRT2.1
show a rapid induction of gene expression in re-
sponse to nitrate treatments independent of protein
T101 is not phosphorylated, NRT1.1 functions as a
low-affinity carrier, and NRT2.1 gene expression is
strongly induced. The NRT1.1 protein is involved
in both nitrate perception and transport (14–16),
functions that can be differentiated by the mutant
allele chl1-9. Chl1-9 carries a point mutation that
tation reduces NRT1.1 nitrate uptake in all affinity
ranges but does not affect the primary nitrate re-
sponse of NRT2.1. Thus, nitrate transport activity is
nitrate as well as other forms of N may yet be dis-
covered in plants. Nitrate induction of NRT2.1 and
other primary response genes is unaffected in nrt1.1
mutants if nitrate treatments are carried out after
N deprivation (14). Genetic evidence supports a
role for NRT2.1 in a signaling pathway that re-
presses lateral root initiation in response to nu-
signal transducer (17).The role of AMMONIUM
TRANSPORTER 1.3 in regulating lateral root
branching in response to ammonium is indepen-
dent of ammonium transport, suggesting a sig-
naling role for this transporter (18).
The first regulatory factor identified in N re-
sponses was the MADS box transcription factor
Transgenic plants with repressed expression levels
notshowthe characteristic root elongation response
tion factors known to regulate N responses include
NIN-LIKE PROTEIN7 (NLP7), required for nor-
ARY DOMAIN (LBD37/38/39), found to re-
press anthocyanin biosynthesis and many other
known N-responsive genes, including key genes
required for nitrate uptake and assimilation (21);
ELONGATED HYPOCOTYL 5 (HY5) and HY5-
REDUCTASE (NIA) 2 and negative regulators
PROMOTER BINDING PROTEIN–LIKE 9, a
negative regulator of NIR and NIA2 (23) (Fig. 1).
Besides transcription, posttranscriptional mech-
anisms are implicated in plant N responses. The
Arabidopsis NITROGEN LIMITATION ADAPTA-
sis and interactions between N and phosphate
metabolism in plants (25). The nitrate-responsive
CIPK8 is required for normal nitrate regulation of
byNlimitation may lead to drought tolerance by
factor crucial for expression of drought-resistance
genes (27) (Fig. 1).
Despite progress in identifying some compo-
nents in regulatory networks, a comprehensive
view of the N signal transduction pathways and
how they impinge upon metabolic and develop-
mental processes is still lacking. What are the
mechanistic relationships between the regulatory
components and response networks identified
thus far (Fig.1)? We know that the Nresponse in
Arabidopsis has an important cell-specific com-
ing of spatiotemporal aspects (2). Where is the
nitrate signalfirstsensed?Howistheresponse of
individual cells orchestrated to articulate organis-
over developmental time? Answering these ques-
tions is important for generating the holistic view
ofplantNnutrition necessary to increase N-use
efficiency in crops.
Systems Biology for Understanding Plant
Systems biology has accelerated the discovery of
knowledge across traditionally disconnected fields
of plant biology (Fig. 2). A systems biology ap-
proach to understanding N-regulatory networks
FONDAP Center for Genome Regulation, Millennium Nucleus
Molecular y Microbiología, Pontificia Universidad Católica de
Chile, Avenida Libertador Bernardo O’Higgins 340, Santiago,
Chile. E-mail: firstname.lastname@example.org
VOL 33629 JUNE 2012
on July 26, 2012
genome-wide information about components
and their relationships in Arabidopsis, together
ments under various N regimes, has provided a
fertile terrain for addressing plant responses to
N. Systems analysis of expression data in Arabi-
dopsis roots identified molecular machines and
cellular processes that are modulated by N and
carbon and N interactions. This analysis high-
lighted the role of auxin and cytokinin signaling
pathways and microRNAs asimportant players in
showed that CIRCADIAN CLOCK ASSOCI-
ATED 1 (CCA1), one of the master regulators of
the circadian clock, coordinates the organic N re-
the promoters of BASIC REGION/LEUCINE ZIP-
in turn regulates ASPARAGINE SYNTHETASE
1 (ASN1) expression), GLUTAMINE SYNTHE-
1 (33). CCA1 thus integrates N nutrition and circa-
(34) (Fig. 2A). Systems analysis provided mech-
anisms to explain howrootsystem architecture is
modulated by N availability. Network analysis
identified miR167 and one of its targets, AUXIN
RESPONSE FACTOR 8 (ARF8), in the control of
(Fig. 2B). Nitrate treatments repressed miR167 in
script. ARF8 induction in pericycle cells triggered
ing lateral roots (28). Another study revealed an
incoherent feed-forward mechanism that is in-
duced by nitrate and repressed by N metabolites
generated by nitrate assimilation (35) (Fig. 2C).
miR393 and one of its targets, the auxin receptor
AFB3 (35). Induction of AFB3 gene expression
by nitrate leads to auxin responses in primary and
lateral roots.Under sufficient N nutrition,miR393
sensitivity. This regulatory module is a simple
mechanism that controls root system architecture
in response to external and internal N availability
of systems biology to address molecular mech-
anisms as well as to connect distinct biological
processes. These findings represent first steps to
N-use efficiency in crop production systems.
World population is estimated to reach 9 billion
inhabitants by 2050 and more beyond (36). In-
creased needs for food will impose a large stress
of crops—for example, for biofuel production—
will also tax agricultural systems. Besides the di-
rect implications for crop yield, the interactions
between the nitrogen and carbon cycle are key
players in Earth’s climate and other planetary pro-
cesses (4). The magnitude and seriousness of this
challenge must not be underestimated. Increased
understanding of N-use efficiency for increased
Primary nitrate response
Primary root growth
Genes related to
N stress adaption
Fig. 1. A simplified summary of known regulatory components controlling
Arabidopsis responses to N. At the perception layer, NRT1.1 stands out as the
studies identified transcription factors and other putative components of N
signaling pathways, mostly in Arabidopsis thaliana. Response networks cor-
respond tometabolic,physiological,and growth and developmentalpathways
activated for adaptive responses to changes in N availability. Only responses
that can be connected to upper regulatory components are shown. (A) Under
high-nitrate conditions (>1 mM), NRT1.1 transporter functions as a low-
affinity nitrate transporter. (B) Under low-nitrate conditions (<1 mM), NRT1.1
transporter is phosphorylated at T101 and functions as a high-affinity nitrate
Green shapes represent transcription factors, gray octagons represent en-
regulatory molecules. Black lines represent relationships obtained by mo-
lecular genetic approaches, and red lines represent relationships discovered
by systems biology approaches.
29 JUNE 2012VOL 336
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a complex trait controlled by interwoven networks
tal pathways. Environmental interactions and cell-,
tissue-, andorgan-specific adaptiveresponsesfor a
given genotype add nuances. Traditional trial-and-
error approaches to addressing N-use efficiency
ing intricate metabolic or regulatory networks, we
must consider the system-wide implications of our
alterations under a wide range of environmental
should be harnessed.
Systems biology approaches are building a ho-
listic understanding of N-regulatory networks and
molecular mechanisms to control growth and de-
velopment in plants. Ultimately, systems biology
be used for in silico design and testing of network
alterations.Thenewresearch fieldofsynthetic biol-
ogy can leverage this knowledge for biological en-
bust biological functions to construct devices and
circuits with new properties [e.g., (38)]. There is a
Akey bottleneck to advances in synthetic biology
community should embrace the development of
synthetic biologydesignprinciplesand standards
should help both advance our understanding of
plant biology as well as facilitate design and con-
N-use efficiency in crop production systems.
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Acknowledgments: Thanks to N. Crawford and Y.-F. Tsay for
critical comments on the manuscript. Thanks also to J. M. Alvarez,
E. Vidal, and O. Contreras for figures and constructive
discussions. Research in our group is funded by International Early
Career Scientist program from Howard Hughes Medical Institute,
Fondo de Desarrollo de Areas Prioritarias (FONDAP) Center for
Genome Regulation (15090007), Millennium Nucleus Center for
Plant Functional Genomics (P10-062-F), Fondo Nacional de
Desarrollo Científico y Tecnológico (1100698), Comisión Nacional
de Investigación Científica y Tecnológica-ANR program (ANR-007),
and Corporación de Fomento de la Producción Genome
Organic N NO3
Auxin response networks
Auxin response networks
Organic N NO3
Fig. 2. Systems biology approaches tomap N-regulatory networks.Systems biol-
ogy approaches accelerate discovery of N-regulatory networks as well as connect
connection between genes in the N-assimilation pathway and the circadian clock.
to the clock. (B) A type I incoherent feed-forward loop motif including miR393
Organic N affects lateral root growth through an independent pathway that
requires miR167 and ARF8. (C) The miR393/AFB3 regulatory motif is also im-
Glu) to adjust primary root growth based on N demand.
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