Skip to main content
SpringerLink
Log in

Molecular cloning and characterization of phosphorus starvation responsive genes in common bean (Phaseolus vulgaris L.)

  • Original Article
  • Published:
Planta Aims and scope Submit manuscript

Abstract

Common bean (Phaseolus vulgaris L.) is one of the most important food legumes in the world and its production is limited by low phosphate (Pi) availability in many arable soils. To gain better insight into the molecular mechanisms by which common bean adapts to low Pi availability, we generated a suppression subtractive cDNA library to identify genes involved in P starvation responses. Over 240 putative Pi starvation-responsive genes were identified. The identified clones were sequenced and BLASTx/BLASTn analysis revealed an array of 82 genes showing a high degree of sequence homology to known and unknown proteins in the database. Transcript abundance of seven genes representing different functional categories was examined by Northern blot analysis. Six genes were strongly induced/enhanced under Pi deficiency confirming the results of SSH. Full length cDNAs for three genes, representing PvIDS4-like, PvPS2, and PvPT1 were cloned and characterized. The open reading frame (ORF) of PvIDS4-like encodes a 281-amino acid protein, containing a SPX domain. The ORF of PvPS2 gene encodes a 271-amino acid protein coding for a putative phosphatase. The PvPT1 encodes a 531-amino acid protein exhibiting high homology with high affinity Pi transporters. Expression patterns of these three genes in relation to Pi availability were evaluated with two contrasting genotypes (P-inefficient Dor364 and P-efficient G19833). Both Northern and RT-PCR results showed enhanced accumulation of phosphate transporters and phosphatases in P-efficient genotype, implying that in addition to modified root morphology and architecture, increased P transport and phosphatases activity might contribute to efficient Pi acquisition and translocation in G19833 common bean genotype under limited Pi conditions.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9

Similar content being viewed by others

Abbreviations

Pi:

Phosphate

PvIDS-4:

Phaseolus vulgarisIron Deficiency Specific-4 like gene

PvPS-2:

Phaseolus vulgarisPhosphate Starvation induced-2 gene

PvPT-1:

Phaseolus vulgarisPi Transporter-1

SSH:

Suppression subtractive hybridization

ORF:

Open-reading frame

bp:

Base pairs

RT-PCR:

Reverse transcriptase polymerase chain reaction

References

  • Abel S, Ticconi CA, Delatorre CA (2002) Phosphate sensing in higher plants. Physiol Plant 115:1–8

    Article  PubMed  CAS  Google Scholar 

  • Baldwin JC, Karthikeyan AS, Raghothama KG (2001) LEPS2, a phosphorus starvation-induced novel acid phosphatase from tomato. Plant Physiol 125:728–737

    Article  PubMed  CAS  Google Scholar 

  • Beebe S, Lynch J, Galwey N, Tohme J, Ochoa I (1997) A geographical approach to identify P-efficient genotypes among landraces and wild ancestors of common bean. Euphytica 95:325–336

    Article  Google Scholar 

  • Beebe SE, Rojas-Pierce M, Yan XL, Blair MW, Pedraza F, Muñoz F, Tohme J, Lynch JP (2006) Quantitative trait loci for root architecture traits correlated with phosphorus acquisition in common bean. Crop Sci 46:413–423

    Article  CAS  Google Scholar 

  • Burleigh SH, Harrison MJ (1998) Characterization of the Mt4 gene from Medicago truncatula. Gene 216:47–53

    Article  PubMed  CAS  Google Scholar 

  • Diatchenko L, Lau YF, Campbell AP, Chenchik A, Moqadam F, Huang B, Lukyanov S, Lukyanov K, Gurskaya N, Sverdlov ED, Siebert PD (1996) Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Natl Acad Sci USA 93:6025–6030

    Article  PubMed  CAS  Google Scholar 

  • Duff SMG, Moorhead GBG, Lefebvre DD, Plaxton WC (1989) Phosphate starvation inducible “bypasses” of adenylate and phosphate dependent glycolytic enzymes in Brassica nigra suspension cells. Plant Physiol 90:1275–1278

    Article  PubMed  CAS  Google Scholar 

  • Fan M, Zhu J, Richards C, Brown KM, Lynch JP (2003) Physiological roles for aerenchyma in phosphorus-stressed roots. Fun Plant Biol 30:493–506

    Article  Google Scholar 

  • Graham MA, Ramírez M, Vald´Es-L´Opez O, Larab M, Tesfaye M, Vance CP, Hernandez G (2006) Identification of candidate phosphorus stress induced genes in Phaseolus vulgaris through clustering analysis across several plant species. Fun Plant Biol 33:789–797

    Article  CAS  Google Scholar 

  • Hamburger D, Rezzonico E, MacDonald-Comber PJ, Somerville C, Poirier Y (2002) Identification and characterization of the Arabidopsis PHO1 gene involved in phosphate loading to the xylem. Plant Cell 14:889–902

    Article  PubMed  CAS  Google Scholar 

  • Hammond JP, Bennett MJ, Bowen HC, Broadley MR, Eastwood DC, May ST, Rahn C, Swarup R, Woolaway KE, White PJ (2003) Changes in gene expression in Arabidopsis shoots during phosphate starvation and the potential for developing smart plants. Plant Physiol 132:578–596

    Article  PubMed  CAS  Google Scholar 

  • Harrison MJ, Dewbre GR, Liu J (2002) A phosphate transporter from Medicago truncatula involved in the acquisition of phosphate released by arbuscular mycorrhizal fungi. Plant Cell 14:2413–2429

    Article  PubMed  CAS  Google Scholar 

  • Hou XL, Wu P, Jiao FC, Jia QJ, Chen HM, Yu J, Song XW, Yi KK (2005) Regulation of the expression of OsIPS1 and OsIPS2 in rice via systemic and local Pi signaling and hormones. Plant Cell Environ 28:353–364

    Article  CAS  Google Scholar 

  • Hu WW, Gong HB, Pua EC (2005) The pivotal roles of the plant S-adenosylmethionine decarboxylase 5′ untranslated leader sequence in regulation of gene expression at the transcriptional and posttranscriptional levels. Plant Physiol 138:276–286

    Article  PubMed  CAS  Google Scholar 

  • Jain A, Vasconcelos MM, Raghothama KG, Sahi SV (2007) Molecular mechanisms of plant adaptation to phosphate deficiency. Plant Breed Rev 29:359–419

    Article  CAS  Google Scholar 

  • Juszczuk I, Malusà E, Rychter AM (2001) Oxidative stress during phosphate deficiency in roots of bean plants (Phaseolus vulgaris L.). J Plant Physiol 158:1299−1305

    Article  CAS  Google Scholar 

  • Karthikeyan AS, Varadarajan DK, Mukatira UT, D’Urzo M P, Damaz B, Raghothama KG (2002) Regulated expression of Arabidopsis phosphate transporters. Plant Physiol 130:221–233

    Article  PubMed  CAS  Google Scholar 

  • Kock M, Stenzel I, Zimmer A (2006) Tissue-specific expression of tomato Ribonuclease LX during phosphate starvation-induced root growth. J Exp Bot 57:3717–3726

    Article  PubMed  CAS  Google Scholar 

  • Kondracka A, Rychter AM (1997) The role of Pi recycling processes during photosynthesis in phosphate-deficient bean plants. J Exp Bot 48:1461–1468

    Article  CAS  Google Scholar 

  • Liao H, Rubio G, Yan X, Cao A, Brown K, Lynch JP (2001) Effect of phosphorus availability on basal root shallowness in common bean. Plant Soil 232:69–79

    Article  PubMed  CAS  Google Scholar 

  • Liao H, Yan XL, Rubio G, Beebe SE, Blair MW, Lynch JP (2004) Genetic mapping of basal root gravitropism and phosphorus acquisition efficiency in common bean. Funct Plant Biol 31:959–970

    Article  CAS  Google Scholar 

  • Liu C, Muchhal US, Raghothama KG (1997) Differential expression of TPS11, a phosphate starvation-induced gene in tomato. Plant Mol Biol 33:867–874

    Article  PubMed  CAS  Google Scholar 

  • Liu CM, Muchhal US, Mukatira U, Kononowicz AK, Raghothama KG (1998) Tomato phosphate transporter genes are differentially regulated in plant tissues by phosphorus. Plant Physiol 116:91–99

    Article  PubMed  CAS  Google Scholar 

  • Morcuende R, Bari R, Gibon Y, Zheng W, Datt Pant B, Bläsing O, Usadel B, Czechowski T, Udvardi MK, Stitt M, Scheible WR (2007) Genome-wide reprogramming of metabolism and regulatory networks of Arabidopsis in response to phosphorus. Plant Cell Environ 30:85–112

    Article  PubMed  CAS  Google Scholar 

  • Misson J, Raghothama KG, Jain A, Jouhet J, Block MA, Bligny R, Ortet P, Creff A, Somerville S, Rolland N, Doumas P, Nacry P, Herrerra-Estrella L, Nussaume L, Thibaud MC (2005) A genome-wide transcriptional analysis using Arabidopsis thaliana Affymetrix gene chips determined plant responses to phosphate deprivation. Proc Natl Acad Sci USA 102:11934–11939

    Article  PubMed  CAS  Google Scholar 

  • Muchhal US, Pardo JM, Raghothama KG (1996) Phosphate transporters from the higher plant Arabidopsis thaliana. Proc Natl Acad Sci USA 93:10519–10523

    Article  PubMed  CAS  Google Scholar 

  • Murphy J, Riley J (1963) A modified single solution for the determination of phosphate in natural waters. Anal Chim Acta 27:31–35

    Article  Google Scholar 

  • Pieters AJ, Paul MJ, Lawlor DW (2001) Low sink demand limits photosynthesis under Pi deficiency. J Exp Bot 52:1083–1091

    Article  PubMed  CAS  Google Scholar 

  • Plaxton WC, Carswell MC (1999) Metabolic aspects of the phosphate starvation response in plants. In: Lerner HR (eds) Plant responses to environmental stresses: From Phytohormones to Genome Reorganization. New York, pp 349–372

  • Raghothama KG (1999) Phosphate acquisition. Annu Rev Plant Physiol Plant Mol Biol 50:665–93

    Article  PubMed  CAS  Google Scholar 

  • Raghothama KG, Karthikeyan AS (2005) Phosphate acquisition. Plant Soil 274:37–49

    Article  CAS  Google Scholar 

  • Ramírez M, Graham MA, Blanco-LÓpez L, Silvente S, Medrano-Soto A, Blair MW, Hernández G, Vance CP, Lara M (2005) Sequencing and analysis of common bean ESTs building a foundation for functional genomics. Plant Physiol 137:1211–1227

    Article  PubMed  CAS  Google Scholar 

  • Shen H, Yan XL, Zhao M, Zheng SL, Wang XR (2002) Exudation of organic acids in common bean as related to mobilization of aluminum- and iron-bound phosphates. Environ Exp Bot 48:1–9

    Article  CAS  Google Scholar 

  • Shin H, Shin HS, Chen RJ, Harrison MJ (2006) Loss of At4 function impacts phosphate distribution between the roots and the shoots during phosphate starvation. Plant J 45:712–726

    Article  PubMed  CAS  Google Scholar 

  • Srivastava AK, Venkatachalam P, Raghothama KG, Sahi SV (2007) Identification of lead-regulated genes by suppression subtractive hybridization in the heavy metal accumulator Sesbania drummondii. Planta 225:1353–1365

    Article  PubMed  CAS  Google Scholar 

  • Stenzel I, Ziethe K, Schurath J, Hertel SC, Bosse D, Köck M (2003) Differential expression of the LePS2 phosphatase gene family in response to phosphate availability, pathogen infection and during development. Physiol Plant 118:138–146

    Article  PubMed  CAS  Google Scholar 

  • Thomas C, Sun Y, Naus K, Lloyd A, Roux S (1999) Apyrase functions in plant phosphate nutrition and mobilizes phosphate from extracellular ATP. Plant Physiol 119:543–551

    Article  PubMed  CAS  Google Scholar 

  • Uhde-Stone C, Zinn KE, Ramirez-Yanez M, Li A, Vance CP, Allan DL (2003) Nylon filter arrays reveal differential gene expression in proteoid roots of white lupin in response to phosphorus deficiency. Plant Physiol 131:1064–1079

    Article  PubMed  CAS  Google Scholar 

  • Vance CP, Uhde-Stone C, Allen DL (2003) P acquisition and use: critical adaptations by plants for securing a nonrenewable resource. New Phytol 157:423–447

    Article  CAS  Google Scholar 

  • Venkatachalam P, Thulaseedharan A, Raghothama KG (2007) Identification of expression profiles of tapping panel dryness (TPD) associated genes from the latex of rubber tree (Hevea brasiliensis Muell. Arg.). Planta 226:499–515

    Article  PubMed  CAS  Google Scholar 

  • Wang YH, Garvin DF, Kochian LV (2002) Rapid induction of regulatory and transporter genes in response to phosphorus, potassium, and iron deficiencies in tomato roots. Evidence for cross talk and root/rhizosphere-mediated signals. Plant Physiol 130:1361–1370

    Article  PubMed  CAS  Google Scholar 

  • Wang Y, Ribot C, Rezzonico E, Poirier Y (2004) Structure and expression profile of the arabidopsis PHO1 gene family indicates a broad role in inorganic phosphate homeostasis. Plant Physiol 135:400–411

    Article  PubMed  CAS  Google Scholar 

  • Wasaki J, Shinano T, Onishi K, Yonetani R, Yazaki J, Fujii F, Shimbo K, Ishikawa M, Shimatani Z, Nagata Y, Hashimoto A, Ohta T, Sato Y, Miyamoto C, Honda S, Kojima K, Sasaki T, Kishimoto N, Kikuchi S, Osaki M (2006) Transcriptomic analysis indicates putative metabolic changes caused by manipulation of phosphorus availability in rice leaves. J Exp Bot 57:2049–2059

    Article  PubMed  CAS  Google Scholar 

  • Wu P, Ma LG, Hou XL, Wang MY, Wu YR, Liu FY, Deng XW (2003) Phosphate starvation triggers distinct alterations of genome expression in Arabidopsis roots and leaves. Plant Physiol 132:1260–1271

    Article  PubMed  CAS  Google Scholar 

  • Wykoff DD, O’Shea EK (2001) Phosphate transport and sensing in Saccharomyces cerevisiae. Genetics 159:1491–1499

    PubMed  CAS  Google Scholar 

  • Yan XL, Lynch JP, Beebe SE (1995a) Phosphorus efficiency in common bean genotypes in contrasting soil types. I. Vegetative response. Crop Sci 35:1086–1093

    Article  Google Scholar 

  • Yan XL, Beebe SE, Lynch JP (1995b) Phosphorus efficiency in common bean genotypes in contrasting soil types. II. Yield response. Crop Sci 35:1094–1099

    Article  Google Scholar 

  • Yan XL, Liao H, Trull MC, Beebe SE, Lynch JP (2001) Induction of a major leaf acid phosphates does not confer adaptation to low P availability in common bean. Plant Physiol 125:1901–1911

    Article  PubMed  CAS  Google Scholar 

  • Yan XL, Liao H, Beebe SE, Blair MW, Lynch JP (2004) QTL mapping of root hair and acid exudation traits and their relationship to phosphorus uptake in common bean. Plant Soil 265:17–29

    Article  CAS  Google Scholar 

  • Yun SJ, Kaeppler SM (2001) Induction of maize acid phosphatase activities under phosphorus starvation. Plant Soil 237:109–115

    Article  CAS  Google Scholar 

  • Zhang Y, Mian MAR, Chekhovskiy K, So S, Kupfer D, Lai HS, Roe BA (2005) Differential gene expression in Festuca under heat stress conditions. J Exp Bot 56:897–907

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

This research is in part supported by funds from the Collaborative Crop Research Program of the McKnight Foundation to K. G. Raghothama and X. L. Yan and the Key Basic Research Special Funds of China to X. L. Yan (2005CB120902).

Author information

Authors and Affiliations

  1. Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47906, USA

    Jiang Tian, Perumal Venkatachalam & Kashchandra Raghothama

  2. Laboratory of Plant Nutritional Genetics, Root Biology Center, South China Agricultural University, Guangzhou, 510642, China

    Jiang Tian, Hong Liao & Xiaolong Yan

Authors
  1. Jiang Tian
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Perumal Venkatachalam
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hong Liao
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Xiaolong Yan
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Kashchandra Raghothama
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Xiaolong Yan or Kashchandra Raghothama.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplement Figures (DOC 44 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Tian, J., Venkatachalam, P., Liao, H. et al. Molecular cloning and characterization of phosphorus starvation responsive genes in common bean (Phaseolus vulgaris L.). Planta 227, 151–165 (2007). https://doi.org/10.1007/s00425-007-0603-2

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00425-007-0603-2

Keywords

Search

Navigation