Sequencing and Phylogenetic Analysis of nodC Gene from Pea Rhizobium

Javaria Tabusam¹ , Nisar Ahmed² , Umer Karamat³ , Nasar Amjad⁴ , Hafiza Hadiqa Anum⁵ , Sumer Zulfiqar⁶

Section:Research Paper, Product Type: Journal-Paper
Vol.7 , Issue.6 , pp.95-106, Dec-2020

Online published on Dec 31, 2020

Copyright © Javaria Tabusam, Nisar Ahmed, Umer Karamat, Nasar Amjad, Hafiza Hadiqa Anum, Sumer Zulfiqar . This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
 

View this paper at   Google Scholar | DPI Digital Library

XML View     PDF Download

How to Cite this Paper

Abstract :
Pea is a legume that belongs to the family Fabaceae and an economical source of carbohydrates, proteins, and vitamins. Nitrogen deficiency is the main problem of crops, which is hard to overcome. However, pea plants can establish a symbiotic relationship with the bacteria known as Rhizobacterium and efficiently utilize the available nitrogen through the roots, and the plant can withstand even harsh conditions. Nodule, which is established by these rhizobacteria are main parts which are involved in the process of nitrogen fixation; Nod factors are stimulator for the establishment of nodules in the rhizobia of pea NodC gene is one of these factors, used as a genetic marker to analyze the genetic variation among Rhizobacterium keeping in view the capability of nitrogen fixation. In this purposed research, the nodC gene was amplified using PCR technology, cloning, sequencing, and phylogenetic analysis to study the homology and divergence in Rhizobium from other species that have these Nod factors in establishing the nodulation and enhancing the nitrogen fixation in the leguminous species.

Key-Words / Index Term :
Pea, Phylogenetic analysis, NodC Gene, Rhizobium

References :
[1] B. Vanlauwe, M. Hungria, F. Kanampiu, K.E. Giller, "The role of legumes in the sustainable intensification of African smallholder agriculture: Lessons learnt and challenges for the future", Agriculture, Ecosystems & Environment, Vol.284, pp.106583, 2019.
[2] J.I. Sprent, J. Ardley, E.K. James, "Biogeography of nodulated legumes and their nitrogen?fixing symbionts", New Phytologist, Vol.215, Issue.1, pp.40-56, 2017.
[3] M.H. Sarwar, M.F. Sarwar, M. Sarwar, N.A. Qadri, S. Moghal, "The importance of cereals (Poaceae: Gramineae) nutrition in human health: A review", Journal of cereals and oilseeds, Vol.4, Issue.3, pp.32-35, 2013.
[4] K.-H. Jung, G. An, P.C. Ronald, "Towards a better bowl of rice: assigning function to tens of thousands of rice genes", Nature Reviews Genetics, Vol.9, Issue.2, pp.91-101, 2008.
[5] J. Burstin, P. Marget, M. Huart, A. Moessner, B. Mangin, C. Duchene, B. Desprez, N. Munier-Jolain, G. Duc, "Developmental genes have pleiotropic effects on plant morphology and source capacity, eventually impacting on seed protein content and productivity in pea", Plant physiology, Vol.144, Issue.2, pp.768-781, 2007.
[6] R. Bora, C. Sarma, "Effect of gibberellic acid and cycocel on growth, yield and protein content of pea", Asian Journal of Plant Sciences, 2006.
[7] C. Masson-Boivin, E. Giraud, X. Perret, J. Batut, "Establishing nitrogen-fixing symbiosis with legumes: how many rhizobium recipes?", Trends in microbiology, Vol.17, Issue.10, pp.458-466, 2009.
[8] E.D. Bobo, P. Jinga, N. Muzvidzwa, G. Zingoni, P. Munosiyei, E. Zingoni Assessment of Nodulation Potential of Bradyrhizobium japonicum and Bradyrhizobium elkanii on Glycine max L. in Acidic Clay and Loam Soils, International Journal of Scientific Research in Biological Sciences, Vol.7, Issue.3, pp.47-51, 2020.
[9] G. Rajendran, S. Mistry, A.J. Desai, G. Archana, "Functional expression of Escherichia colifhuA gene in Rhizobium spp. of Cajanus cajan provides growth advantage in presence of Fe 3+: ferrichrome as iron source", Archives of microbiology, Vol.187, Issue.4, pp.257, 2007.
[10] G. Rajendran, F. Sing, A.J. Desai, G. Archana, "Enhanced growth and nodulation of pigeon pea by co-inoculation of Bacillus strains with Rhizobium spp", Bioresource technology, Vol.99, Issue.11, pp.4544-4550, 2008.
[11] Y. Zhou, Y. Zhang, J. Wei, Y. Zhang, J. Li, W. Wang, H. Duan, J. Chen, "Cloning and analysis of expression patterns and transcriptional regulation of RghBNG in response to plant growth regulators and abiotic stresses in Rehmannia glutinosa", Springerplus, Vol.4, Issue.1, pp.60, 2015.
[12] E.M. Lodwig, A.H. Hosie, A. Bourdes, K. Findlay, D. Allaway, R. Karunakaran, J. Downie, P.S. Poole, "Amino-acid cycling drives nitrogen fixation in the legume–Rhizobium symbiosis", Nature, Vol.422, Issue.6933, pp.722-726, 2003.
[13] G. Centenaro, C. Hudek, A. Zanella, A. Crivellaro, "Root-soil physical and biotic interactions with a focus on tree root systems: A review", Applied Soil Ecology, Vol.123, pp.318-327, 2018.
[14] R. Rivas, M. Laranjo, P. Mateos, S. Oliveira, E. Martínez?Molina, E. Velázquez, "Strains of Mesorhizobium amorphae and Mesorhizobium tianshanense, carrying symbiotic genes of common chickpea endosymbiotic species, constitute a novel biovar (ciceri) capable of nodulating Cicer arietinum", Letters in applied microbiology, Vol.44, Issue.4, pp.412-418, 2007.
[15] C. Silva, P. Vinuesa, L.E. Eguiarte, E. Martínez-Romero, V. Souza, "Rhizobium etli and Rhizobium gallicum nodulate common bean (Phaseolus vulgaris) in a traditionally managed milpa plot in Mexico: population genetics and biogeographic implications", Applied and environmental microbiology, Vol.69, Issue.2, pp.884-893, 2003.
[16] P. Garcia-Fraile, D. Mulas-Garcia, A. Peix, R. Rivas, F. Gonzalez-Andres, E. Velazquez, "Phaseolus vulgaris is nodulated in northern Spain by Rhizobium leguminosarum strains harboring two nodC alleles present in American Rhizobium etli strains: biogeographical and evolutionary implications", Canadian journal of microbiology, Vol.56, Issue.8, pp.657-666, 2010.
[17] G. Bena, A. Lyet, T. Huguet, I. Olivieri, "Medicago–Sinorhizobium symbiotic specificity evolution and the geographic expansion of Medicago", Journal of Evolutionary Biology, Vol.18, Issue.6, pp.1547-1558, 2005.
[18] F. Debelle, C. Rosenberg, J. Denarié, "The Rhizobium, Bradyrhizobium, and Azorhizobium NodC proteins are homologous to yeast chitin synthases", MOLECULAR PLANT MICROBE INTERACTIONS, Vol.5, pp.443-443, 1992.
[19] F. Mus, M.B. Crook, K. Garcia, A.G. Costas, B.A. Geddes, E.D. Kouri, P. Paramasivan, M.-H. Ryu, G.E. Oldroyd, P.S. Poole, "Symbiotic nitrogen fixation and the challenges to its extension to nonlegumes", Applied and environmental microbiology, Vol.82, Issue.13, pp.3698-3710, 2016.
[20] J. Angelini, S. Castro, A. Fabra, "Alterations in root colonization and nodC gene induction in the peanut–rhizobia interaction under acidic conditions", Plant Physiology and Biochemistry, Vol.41, Issue.3, pp.289-294, 2003.
[21] B. Gourion, F. Berrabah, P. Ratet, G. Stacey, "Rhizobium–legume symbioses: the crucial role of plant immunity", Trends in plant science, Vol.20, Issue.3, pp.186-194, 2015.
[22] R.F. Fisher, J.K. Tu, S.R. Long, "Conserved Nodulation Genes in Rhizobium meliloti and Rhizobium trifolii", Applied and Environmental Microbiology, Vol.49, Issue.6, pp.1432-1435, 1985.
[23] N. Peters, D. Verma, "Phenolic compounds as regulators of gene expression in plant-microbe interactions", Mol Plant-Microbe Interact, Vol.3, pp.4-8, 1990.
[24] X. Perret, C. Staehelin, W.J. Broughton, "Molecular basis of symbiotic promiscuity", Microbiology and Molecular Biology Reviews, Vol.64, Issue.1, pp.180-201, 2000.
[25] R. Poupot, E. Martinez-Romero, J.C. Prome, "Nodulation factors from Rhizobium tropici are sulfated or nonsulfated chitopentasaccharides containing an N-methyl-N-acylglucosaminyl terminus", Biochemistry, Vol.32, Issue.39, pp.10430-10435, 1993.
[26] R. Poupot, E. Martinez-Romero, N. Gautier, J.-C. Promé, "Wild type Rhizobium etli, a bean symbiont, produces acetyl-fucosylated, N-methylated, and carbamoylated nodulation factors", Journal of Biological Chemistry, Vol.270, Issue.11, pp.6050-6055, 1995.
[27] P. Rahi, R. Kapoor, J. Young, A. Gulati, "A genetic discontinuity in root?nodulating bacteria of cultivated pea in the Indian trans?Himalayas", Molecular Ecology, Vol.21, Issue.1, pp.145-159, 2012.
[28] J.M. Vincent, "A manual for the practical study of the root-nodule bacteria", A manual for the practical study of the root-nodule bacteria, 1970.
[29] N.D. Marsudi, A.R. Glenn, M.J. Dilworth, "Identification and characterization of fast-and slow-growing root nodule bacteria from South-Western Australian soils able to nodulate Acacia saligna", Soil Biology and Biochemistry, Vol.31, Issue.9, pp.1229-1238, 1999.
[30] H. Sambrook, "Molecular cloning: a laboratory manual. Cold Spring Harbor, NY", 1989.
[31] G. Laguerre, S.M. Nour, V. Macheret, J. Sanjuan, P. Drouin, N. Amarger, "Classification of rhizobia based on nodC and nifH gene analysis reveals a close phylogenetic relationship among Phaseolus vulgaris symbiontsThe GenBank accession numbers for the sequences reported in this paper are AF217261 through AF217272 for nodC and AF218126, AF275670 and AF275671 for nifH", Microbiology, Vol.147, Issue.4, pp.981-993, 2001.
[32] F. Silva, J. Simões-Araújo, J. Silva Júnior, G. Xavier, N. Rumjanek, "Genetic diversity of Rhizobia isolates from Amazon soils using cowpea (Vigna unguiculata) as trap plant", Brazilian Journal of Microbiology, Vol.43, Issue.2, pp.682-691, 2012.
[33] Z. Topcu, "An optimized recipe for cloning of the polymerase chain reaction-amplified DNA inserts into plasmid vectors", Acta Biochimica Polonica, Vol.47, Issue.3, pp.841-846, 2000.
[34] L. Lakatos, G. Szittya, D. Silhavy, J. Burgyán, "Molecular mechanism of RNA silencing suppression mediated by p19 protein of tombusviruses", The EMBO journal, Vol.23, Issue.4, pp.876-884, 2004.
[35] X. Chen, X. Ding, W.-Y. Song, "Isolation of Plasmid DNA rescued from single colonies ofAgrobacterium tumefaciens by means of rolling circle amplification", Plant Molecular Biology Reporter, Vol.21, Issue.4, pp.411-415, 2003.
[36] J.-F. Li, E. Park, A.G. von Arnim, A. Nebenführ, "The FAST technique: a simplified Agrobacterium-based transformation method for transient gene expression analysis in seedlings of Arabidopsis and other plant species", Plant Methods, Vol.5, Issue.1, pp.6, 2009.
[37] M.A. Graham, K.A.T. Silverstein, S.B. Cannon, K.A. VandenBosch, "Computational Identification and Characterization of Novel Genes from Legumes", Plant Physiology, Vol.135, Issue.3, pp.1179-1197, 2004.
[38] M.K. Litvaitis, "A molecular test of cyanobacterial phylogeny: inferences from constraint analyses", Hydrobiologia, Vol.468, Issue.1, pp.135-145, 2002.
[39] M. Yadegari, H.A. Rahmani, G. Noormohammadi, A. Ayneband, "Evaluation of bean (Phaseolus vulgaris) seeds inoculation with Rhizobium phaseoli and plant growth promoting rhizobacteria on yield and yield components", Pakistan journal of biological sciences : PJBS, Vol.11, Issue.15, pp.1935-1939, 2008.
[40] Minaxi, L. Nain, R.C. Yadav, J. Saxena, "Characterization of multifaceted Bacillus sp. RM-2 for its use as plant growth promoting bioinoculant for crops grown in semi arid deserts", Applied Soil Ecology, Vol.59, pp.124-135, 2012.
[41] J.K. Vessey, "Plant growth promoting rhizobacteria as biofertilizers", Plant and Soil, Vol.255, Issue.2, pp.571-586, 2003.
[42] B. Saharan, V. Nehra, "Plant growth promoting rhizobacteria: a critical review", Life Sci Med Res, Vol.21, Issue.1, pp.30, 2011.
[43] C.P. Vance, "Symbiotic nitrogen fixation and phosphorus acquisition. Plant nutrition in a world of declining renewable resources", Plant physiology, Vol.127, Issue.2, pp.390-397, 2001.
[44] N. Parmar, K. Dadarwal, "Stimulation of plant growth of chickpea by inoculation of fluorescent pseudomonads", J Appl Microbiol, Vol.86, pp.36-44, 2000.
[45] M. Naveed, I. Mehboob, M.A. Shaker, M.B. Hussain, M. Farooq, "Biofertilizers in Pakistan: initiatives and limitations", International Journal of Agriculture and Biology, Vol.17, Issue.3, pp.411-420, 2015.
[46] J.E. Clarridge, "Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases", Clinical microbiology reviews, Vol.17, Issue.4, pp.840-862, 2004.
[47] C. Petti, C.R. Polage, P. Schreckenberger, "The role of 16S rRNA gene sequencing in identification of microorganisms misidentified by conventional methods", Journal of clinical microbiology, Vol.43, Issue.12, pp.6123-6125, 2005.
[48] S. Mignard, J.-P. Flandrois, "16S rRNA sequencing in routine bacterial identification: a 30-month experiment", Journal of microbiological methods, Vol.67, Issue.3, pp.574-581, 2006.
[49] D.A. Casamatta, J.R. Johansen, M.L. Vis, S.T. Broadwater, "Molecular and morphological characterization of ten polar and near?polar strains within the Oscillatoriales (Cyanobacteria) 1", Journal of phycology, Vol.41, Issue.2, pp.421-438, 2005.
[50] P. Rajaniemi, J. Komárek, R. Willame, P. Hrouzek, K. Kaštovská, L. Hoffmann, K. Sivonen, "Taxonomic consequences from the combined molecular and phenotype evaluation of selected Anabaena and Aphanizomenon strains", Algological Studies, Vol.117, Issue.1, pp.371-391, 2005.
[51] M.M. Svenning, T. Eriksson, U. Rasmussen, "Phylogeny of symbiotic cyanobacteria within the genus Nostoc based on 16S rDNA sequence analyses", Archives of microbiology, Vol.183, Issue.1, pp.19-26, 2005.
[52] S. Chakravorty, D. Helb, M. Burday, N. Connell, D. Alland, "A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria", Journal of microbiological methods, Vol.69, Issue.2, pp.330-339, 2007.
[53] H.H. Zahran, "Rhizobia from wild legumes: diversity, taxonomy, ecology, nitrogen fixation and biotechnology", Journal of Biotechnology, Vol.91, Issue.2-3, pp.143-153, 2001.
[54] V.K. Chebotar, C.A. Asis, S. Akao, "Production of growth-promoting substances and high colonization ability of rhizobacteria enhance the nitrogen fixation of soybean when coinoculated with Bradyrhizobium japonicum", Biology and Fertility of Soils, Vol.34, Issue.6, pp.427-432, 2001.
[55] A. Valverde, Y. Okon, S. Burdman, "cDNA-AFLP reveals differentially expressed genes related to cell aggregation of Azospirillum brasilense", FEMS microbiology letters, Vol.265, Issue.2, pp.186-194, 2006.
[56] B.S. Mirza, M.S. Mirza, A. Bano, K.A. Malik, "Coinoculation of chickpea with Rhizobium isolates from roots and nodules and phytohormone-producing Enterobacter strains", Australian Journal of Experimental Agriculture, Vol.47, Issue.8, pp.1008-1015, 2007.
[57] K. Raverkar, B. Konde, "Effect of Rhizobium andAzospirillum lipoferum inoculation on the nodulation, yield and nitrogen uptake of peanut cultivars", Plant and soil, Vol.106, Issue.2, pp.249-252, 1988.
[58] K. Rudi, M. Zimonja, B. Kvenshagen, J. Rugtveit, T. Midtvedt, M. Eggesbø, "Alignment-independent comparisons of human gastrointestinal tract microbial communities in a multidimensional 16S rRNA gene evolutionary space", Applied and environmental microbiology, Vol.73, Issue.8, pp.2727-2734, 2007.
[59] V. Ventorino, M. Chiurazzi, M. Aponte, O. Pepe, G. Moschetti, "Genetic diversity of a natural population of Rhizobium leguminosarum bv. viciae nodulating plants of Vicia faba in the Vesuvian area", Current Microbiology, Vol.55, Issue.6, pp.512-517, 2007.
[60] L.A. Mutch, S.M. Tamimi, J. Young, "Genotypic characterisation of rhizobia nodulating Vicia faba from the soils of Jordan: a comparison with UK isolates", Soil Biology and Biochemistry, Vol.35, Issue.5, pp.709-714, 2003.
[61] L.A. Mutch, J.P.W. Young, "Diversity and specificity of Rhizobium leguminosarum biovar viciae on wild and cultivated legumes", Molecular Ecology, Vol.13, Issue.8, pp.2435-2444, 2004.
[62] J.K. Vessey, G.N. Chemining`wa, "The genetic diversity of Rhizobium leguminosarum bv. viciae in cultivated soils of the eastern Canadian prairie", Soil Biology and Biochemistry, Vol.38, Issue.1, pp.153-163, 2006.
[63] G.J. Olsen, C.R. Woese, "Ribosomal RNA: a key to phylogeny", The FASEB journal, Vol.7, Issue.1, pp.113-123, 1993.
[64] Z. Zhang, R.C. Willson, G.E. Fox, "Identification of characteristic oligonucleotides in the bacterial 16S ribosomal RNA sequence dataset", Bioinformatics, Vol.18, Issue.2, pp.244-250, 2002