Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
???displayArticle.abstract???
Setaria viridis is a C4 grass used as a model for bioenergy feedstocks. The elongating internodes in developing S. viridis stems grow from an intercalary meristem at the base, and progress acropetally toward fully expanded cells that store sugar. During stem development and maturation, water flow is a driver of cell expansion and sugar delivery. As aquaporin proteins are implicated in regulating water flow, we analyzed elongating and mature internode transcriptomes to identify putative aquaporin encoding genes that had particularly high transcript levels during the distinct stages of internode cell expansion and maturation. We observed that SvPIP2;1 was highly expressed in internode regions undergoing cell expansion, and SvNIP2;2 was highly expressed in mature sugar accumulating regions. Gene co-expression analysis revealed SvNIP2;2 expression was highly correlated with the expression of five putative sugar transporters expressed in the S. viridis internode. To explore the function of the proteins encoded by SvPIP2;1 and SvNIP2;2, we expressed them in Xenopus laevis oocytes and tested their permeability to water. SvPIP2;1 and SvNIP2;2 functioned as water channels in X. laevis oocytes and their permeability was gated by pH. Our results indicate that SvPIP2;1 may function as a water channel in developing stems undergoing cell expansion and SvNIP2;2 is a candidate for retrieving water and possibly a yet to be determined solute from mature internodes. Future research will investigate whether changing the function of these proteins influences stem growth and sugar yield in S. viridis.
FIGURE 1. Phylogenetic tree based on protein sequences of aquaporins from Setaria viridis and Zea mays.
S. viridis aquaporins were identified in the genome via HMMER search using aquaporins sequences from Arabidopsis, barley, maize, and rice. Maize aquaporins were included in the phylogenetic tree for ease of interpretation. The addition of aquaporin sequences from other grasses did not change the groupings. Tree was generated by neighbor-joining method using the Geneious Tree Builder program, Geneious 9.0.2. The scale bar indicates the evolutionary distance, expressed as changes per amino acid residue. Aquaporins can be grouped into four subfamilies: PIPs (plasma membrane intrinsic proteins), TIPs (tonoplast intrinsic proteins), NIPs (nodulin-like intrinsic proteins), and SIPs (small basic intrinsic proteins). ∗Sevir.5G141800.1 protein sequence is truncated, 112 amino acids in length. ‡SvNIP5;3 (Sevir.6G06000.1) may have a related pseudogene Sevir.6G061300.1.
FIGURE 2. Expression of putative aquaporins across the developmental zones of an elongating S. viridis internode. (A) Schematic of the developmental regions in an elongating internode of S. viridis as reported by Martin et al. (2016): meristematic zone, residing at the base of the internode, where cell division occurs; the cell expansion zone where cells undergo turgor driven expansion; transitional zone where cells begin to differentiate and synthesize secondary cell walls; and the maturation zone whereby expansion, differentiation and secondary cell wall synthesis cease and sugar is accumulated. (B) The expression profiles of putative S. viridis aquaporins, as identified by phylogeny to Z. mays aquaporins, were mined in the S. viridis elongating internode transcriptome (Martin et al., 2016). RNA-seq data is presented as mean FPKM ± SEM for four biological replicates from each developmental zone.
FIGURE 3. Comparison of relative fold changes between RNA-seq and RT-qPCR of SvPIP2;1 and SvNIP2;2 in an elongating internode of S. viridis. (A)
SvPIP2;1. (B)
SvNIP2;2. Data is mean relative fold change in expression ± SEM. Data for RNA-seq and RT-qPCR was normalized relative to the cell expansion zone expression level.
FIGURE 4. Co-expression network of putative S. viridis aquaporin and sugar transporter genes identified in an elongating internode. The co-expressed gene network was generated from the stem specific aquaporins (Figure 2) and sugar transporters identified in the S. viridis elongating internode transcriptome reported by Martin et al. (2016). Raw FPKM values were Log2 transformed and Pearson’s correlation coefficients (0.8–1.0) were calculated in the MetScape app in Cytoscape v3.4.0. Sugar transporters in the S. viridis elongating internode were identified by homology to rice sugar transporter genes (Supplementary Figures S2–S4). Sugar transport related genes are color filled with blue and aquaporin genes with orange. SvNIP2;2 and SvPIP2;1 are in bold font.
FIGURE 5. Osmotic permeability (Pf) of Xenopus laevis oocytes injected with SvNIP2;2 and SvPIP2;1 cRNA. (A) Osmotic permeability (Pf) of water (H2O) injected and SvNIP2;2 and SvPIP2;1 cRNA (46 ng) injected oocytes. Oocytes were transferred into a hypo-osmotic solution, pH 7.4, and Pf was calculated by video monitoring of the rate of oocyte swelling. (B) Effect of lowering oocyte cytosolic pH on osmotic permeability (Pf) of H2O and SvNIP2;2 and SvPIP2;1 cRNA injected oocytes by bathing in hypo-osmotic solution supplemented with 50 mM Na-acetate, pH 5.6, n = 12–14; a = non-significant; b = p < 0.05; c = p < 0.005.
Azad,
Genome-Wide Characterization of Major Intrinsic Proteins in Four Grass Plants and Their Non-Aqua Transport Selectivity Profiles with Comparative Perspective.
2016, Pubmed
Azad,
Genome-Wide Characterization of Major Intrinsic Proteins in Four Grass Plants and Their Non-Aqua Transport Selectivity Profiles with Comparative Perspective.
2016,
Pubmed
Barrieu,
High expression of the tonoplast aquaporin ZmTIP1 in epidermal and conducting tissues of maize.
1998,
Pubmed
Bennetzen,
Reference genome sequence of the model plant Setaria.
2012,
Pubmed
Besse,
Developmental pattern of aquaporin expression in barley (Hordeum vulgare L.) leaves.
2011,
Pubmed
,
Xenbase
Bienert,
A subgroup of plant aquaporins facilitate the bi-directional diffusion of As(OH)3 and Sb(OH)3 across membranes.
2008,
Pubmed
Bienert,
Aquaporin-facilitated transmembrane diffusion of hydrogen peroxide.
2014,
Pubmed
Bihmidine,
Tonoplast Sugar Transporters (SbTSTs) putatively control sucrose accumulation in sweet sorghum stems.
2016,
Pubmed
Bots,
PIP1 and PIP2 aquaporins are differentially expressed during tobacco anther and stigma development.
2005,
Pubmed
,
Xenbase
Brutnell,
Brachypodium distachyon and Setaria viridis: Model Genetic Systems for the Grasses.
2015,
Pubmed
Byrt,
C4 plants as biofuel feedstocks: optimising biomass production and feedstock quality from a lignocellulosic perspective.
2011,
Pubmed
Byrt,
Non-selective cation channel activity of aquaporin AtPIP2;1 regulated by Ca2+ and pH.
2017,
Pubmed
,
Xenbase
Byrt,
Prospecting for Energy-Rich Renewable Raw Materials: Sorghum Stem Case Study.
2016,
Pubmed
Casu,
Identification of transcripts associated with cell wall metabolism and development in the stem of sugarcane by Affymetrix GeneChip Sugarcane Genome Array expression profiling.
2007,
Pubmed
Chaumont,
Plasma membrane intrinsic proteins from maize cluster in two sequence subgroups with differential aquaporin activity.
2000,
Pubmed
,
Xenbase
Chaumont,
Characterization of a maize tonoplast aquaporin expressed in zones of cell division and elongation.
1998,
Pubmed
,
Xenbase
Chaumont,
Aquaporins constitute a large and highly divergent protein family in maize.
2001,
Pubmed
,
Xenbase
Chen,
SWEET sugar transporters for phloem transport and pathogen nutrition.
2014,
Pubmed
Cosgrove,
Biophysical control of plant cell growth.
1986,
Pubmed
Cosgrove,
Growth of the plant cell wall.
2005,
Pubmed
Coskun,
The Role of Silicon in Higher Plants under Salinity and Drought Stress.
2016,
Pubmed
Czechowski,
Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis.
2005,
Pubmed
Danielson,
Unexpected complexity of the aquaporin gene family in the moss Physcomitrella patens.
2008,
Pubmed
De Schepper,
Phloem transport: a review of mechanisms and controls.
2013,
Pubmed
Deshmukh,
Identification and functional characterization of silicon transporters in soybean using comparative genomics of major intrinsic proteins in Arabidopsis and rice.
2013,
Pubmed
,
Xenbase
Eisen,
Cluster analysis and display of genome-wide expression patterns.
1998,
Pubmed
Epstein,
The anomaly of silicon in plant biology.
1994,
Pubmed
Ermawar,
Genetics and physiology of cell wall polysaccharides in the model C4 grass, Setaria viridis spp.
2015,
Pubmed
Fetter,
Interactions between plasma membrane aquaporins modulate their water channel activity.
2004,
Pubmed
,
Xenbase
Finn,
HMMER web server: 2015 update.
2015,
Pubmed
Frick,
Structural basis for pH gating of plant aquaporins.
2013,
Pubmed
Hachez,
The expression pattern of plasma membrane aquaporins in maize leaf highlights their role in hydraulic regulation.
2008,
Pubmed
Hanaoka,
OsNIP3;1, a rice boric acid channel, regulates boron distribution and is essential for growth under boron-deficient conditions.
2014,
Pubmed
Herbers,
Molecular determinants of sink strength.
1998,
Pubmed
Hove,
Identification and Expression Analysis of the Barley (Hordeum vulgare L.) Aquaporin Gene Family.
2015,
Pubmed
Ibraheem,
In silico analysis of cis-acting regulatory elements in 5' regulatory regions of sucrose transporter gene families in rice (Oryza sativa Japonica) and Arabidopsis thaliana.
2010,
Pubmed
Javot,
Role of a single aquaporin isoform in root water uptake.
2003,
Pubmed
Johanson,
The complete set of genes encoding major intrinsic proteins in Arabidopsis provides a framework for a new nomenclature for major intrinsic proteins in plants.
2001,
Pubmed
Johanson,
A new subfamily of major intrinsic proteins in plants.
2002,
Pubmed
Johansson,
Water transport activity of the plasma membrane aquaporin PM28A is regulated by phosphorylation.
1998,
Pubmed
,
Xenbase
Kaldenhoff,
Functional aquaporin diversity in plants.
2006,
Pubmed
Kamiya,
NIP1;1, an aquaporin homolog, determines the arsenite sensitivity of Arabidopsis thaliana.
2009,
Pubmed
,
Xenbase
Karnovsky,
Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data.
2012,
Pubmed
Keegstra,
Plant cell walls.
2010,
Pubmed
Klie,
Identification of superior reference genes for data normalisation of expression studies via quantitative PCR in hybrid roses (Rosa hybrida).
2011,
Pubmed
Krogh,
Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.
2001,
Pubmed
Leitão,
Grapevine aquaporins: gating of a tonoplast intrinsic protein (TIP2;1) by cytosolic pH.
2012,
Pubmed
Lescot,
PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences.
2002,
Pubmed
Li,
The rice aquaporin Lsi1 mediates uptake of methylated arsenic species.
2009,
Pubmed
,
Xenbase
Li,
Setaria viridis and Setaria italica, model genetic systems for the Panicoid grasses.
2011,
Pubmed
Liu,
Characterization and expression of plasma and tonoplast membrane aquaporins in elongating cotton fibers.
2008,
Pubmed
Liu,
Functional divergence of the NIP III subgroup proteins involved altered selective constraints and positive selection.
2010,
Pubmed
Ma,
Transporters of arsenite in rice and their role in arsenic accumulation in rice grain.
2008,
Pubmed
,
Xenbase
Ma,
Functions and transport of silicon in plants.
2008,
Pubmed
Ma,
Characterization of the silicon uptake system and molecular mapping of the silicon transporter gene in rice.
2004,
Pubmed
Ma,
A silicon transporter in rice.
2006,
Pubmed
Malz,
Expression of two PIP genes in rapidly growing internodes of rice is not primarily controlled by meristem activity or cell expansion.
1999,
Pubmed
Martin,
A developing Setaria viridis internode: an experimental system for the study of biomass generation in a C4 model species.
2016,
Pubmed
Maurel,
AQUAPORINS AND WATER PERMEABILITY OF PLANT MEMBRANES.
1997,
Pubmed
,
Xenbase
Maurel,
Molecular physiology of aquaporins in plants.
2002,
Pubmed
Maurel,
Plant aquaporins: membrane channels with multiple integrated functions.
2008,
Pubmed
McCormick,
Supply and demand: sink regulation of sugar accumulation in sugarcane.
2009,
Pubmed
Milne,
Are sucrose transporter expression profiles linked with patterns of biomass partitioning in Sorghum phenotypes?
2013,
Pubmed
Mitani,
Uptake system of silicon in different plant species.
2005,
Pubmed
Mizuno,
The sorghum SWEET gene family: stem sucrose accumulation as revealed through transcriptome profiling.
2016,
Pubmed
Moore,
Developmental changes in cell and tissue water relations parameters in storage parenchyma of sugarcane.
1991,
Pubmed
Mosa,
Members of rice plasma membrane intrinsic proteins subfamily are involved in arsenite permeability and tolerance in plants.
2012,
Pubmed
,
Xenbase
Papini-Terzi,
Sugarcane genes associated with sucrose content.
2009,
Pubmed
Patrick,
Metabolic engineering of sugars and simple sugar derivatives in plants.
2013,
Pubmed
Patrick,
PHLOEM UNLOADING: Sieve Element Unloading and Post-Sieve Element Transport.
1997,
Pubmed
Péret,
Auxin regulates aquaporin function to facilitate lateral root emergence.
2012,
Pubmed
Reinders,
Functional analysis of LjSUT4, a vacuolar sucrose transporter from Lotus japonicus.
2008,
Pubmed
,
Xenbase
Rohwer,
Analysis of sucrose accumulation in the sugar cane culm on the basis of in vitro kinetic data.
2001,
Pubmed
Sakurai,
Identification of 33 rice aquaporin genes and analysis of their expression and function.
2005,
Pubmed
Schmalstig,
Coupling of solute transport and cell expansion in pea stems.
1990,
Pubmed
Schuurmans,
Members of the aquaporin family in the developing pea seed coat include representatives of the PIP, TIP, and NIP subfamilies.
2003,
Pubmed
,
Xenbase
Siefritz,
The tobacco plasma membrane aquaporin NtAQP1.
2001,
Pubmed
,
Xenbase
Slewinski,
Non-structural carbohydrate partitioning in grass stems: a target to increase yield stability, stress tolerance, and biofuel production.
2012,
Pubmed
Slewinski,
Diverse functional roles of monosaccharide transporters and their homologs in vascular plants: a physiological perspective.
2011,
Pubmed
Somerville,
Feedstocks for lignocellulosic biofuels.
2010,
Pubmed
Spyropoulos,
TMRPres2D: high quality visual representation of transmembrane protein models.
2004,
Pubmed
Takano,
The Arabidopsis major intrinsic protein NIP5;1 is essential for efficient boron uptake and plant development under boron limitation.
2006,
Pubmed
,
Xenbase
Tarpley,
Compartmentation of sucrose during radial transfer in mature sorghum culm.
2007,
Pubmed
Tournaire-Roux,
Cytosolic pH regulates root water transport during anoxic stress through gating of aquaporins.
2003,
Pubmed
,
Xenbase
Turgeon,
The puzzle of phloem pressure.
2010,
Pubmed
Törnroth-Horsefield,
Structural mechanism of plant aquaporin gating.
2006,
Pubmed
Uehlein,
The tobacco aquaporin NtAQP1 is a membrane CO2 pore with physiological functions.
2003,
Pubmed
,
Xenbase
Viola,
Tuberization in potato involves a switch from apoplastic to symplastic phloem unloading.
2001,
Pubmed
Vogel,
Unique aspects of the grass cell wall.
2008,
Pubmed
Waclawovsky,
Sugarcane for bioenergy production: an assessment of yield and regulation of sucrose content.
2010,
Pubmed
Wei,
HvPIP1;6, a barley (Hordeum vulgare L.) plasma membrane water channel particularly expressed in growing compared with non-growing leaf tissues.
2007,
Pubmed
,
Xenbase
Welbaum,
Compartmentation of solutes and water in developing sugarcane stalk tissue.
1990,
Pubmed
Werner,
A dual switch in phloem unloading during ovule development in Arabidopsis.
2011,
Pubmed
Wingenter,
Increased activity of the vacuolar monosaccharide transporter TMT1 alters cellular sugar partitioning, sugar signaling, and seed yield in Arabidopsis.
2010,
Pubmed
Yonekura-Sakakibara,
Transcriptome coexpression analysis using ATTED-II for integrated transcriptomic/metabolomic analysis.
2013,
Pubmed
Zelazny,
FRET imaging in living maize cells reveals that plasma membrane aquaporins interact to regulate their subcellular localization.
2007,
Pubmed
,
Xenbase
Zhao,
Involvement of silicon influx transporter OsNIP2;1 in selenite uptake in rice.
2010,
Pubmed
da Silva,
Expression Analysis of Sugarcane Aquaporin Genes under Water Deficit.
2013,
Pubmed