
@article {77381,
	title = {Distinct Evolutionary Origins of Intron Retention Splicing Events in  Antiporter Transcripts Relate to Sequence Specific Distinctions in  Species.},
	journal = {Front Plant Sci},
	volume = {11},
	year = {2020},
	month = {2020},
	pages = {267},
	abstract = {<p>The genome of Asian cultivated rice ( L.) shows the presence of six organelle-specific and one plasma membrane () NHX-type cation proton antiporters. Of these, vacuolar-localized is extensively characterized. The genus consists of 27 species and 11 genome-types, with cultivated rice, diploid , having an AA-type genome. orthologous regions (gene organization, 5{\textquoteright} upstream cis elements, amino acid residues/motifs) from closely related AA genomes cluster distinctly from regions from more ancestral BB, FF and KKLL genomes. These sequence-specific distinctions also extend to two separate intron retention (IR) events involving transcripts that occur at the 5{\textquoteright} and 3{\textquoteright} ends of the NHX1 transcripts. We demonstrate that the IR event involving the 5{\textquoteright} UTR is present only in more recently evolved AA genomes while the IR event governing retention of the 13th intron of (terminal intron) is more ancient in origin, also occurring in halophytic wild rice, (KKLL). We also report presence of a retro-copy of the cDNA in the genome of (). Preferential species and tissue specific up- or down-regulation of the correctly spliced transcript/5{\textquoteright} UTR/13th intron-retaining splice variants under salinity was observed. The implications of IR on mRNA stability and ORF diversity in spp. is discussed.</p>
},
	issn = {1664-462X},
	doi = {10.3389/fpls.2020.00267},
	author = {Sellamuthu, Gothandapani and Jegadeeson, Vidya and Sajeevan, Radha Sivarajan and Rajakani, Raja and Parthasarathy, Pavithra and Raju, Kalaimani and Shabala, Lana and Chen, Zhong-Hua and Zhou, Meixue and Sowdhamini, Ramanathan and Shabala, Sergey and Venkataraman, Gayatri}
}
@article {78101,
	title = {Homology modeling identifies crucial amino-acid residues that confer higher Na+ transport capacity of OcHKT1;5 from Oryza coarctata Roxb.},
	journal = {Plant Cell Physiol},
	year = {2020},
	month = {2020 May 07},
	abstract = {<p>HKT1;5 loci/alleles are important determinants of crop salinity tolerance. HKT1;5s encode plasmalemma-localized Na+-transporters, retrieving xylem Na+ into xylem parenchyma cells, reducing shoot Na+ accumulation. Allelic variation in rice OsHKT1;5 sequence in specific landraces (Nona Bokra OsHKT1;5-NB/Nipponbare OsHKT1;5-Ni) correlates with variation in salt tolerance. Oryza coarctata, a halophytic wild rice, grows in fluctuating salinity at the seawater-estuarine interface in Indian and Bangladeshi coastal regions. The distinct transport characteristics of the shoots and roots expressing O. coarctata OcHKT1;5 transporter, are reported vis-{\`a}-vis OsHKT1;5-Ni. Yeast sodium extrusion-deficient cells expressing\&nbsp;OcHKT1;5 are sensitive to increasing Na+ (10-100 mM). Electrophysiological measurements in Xenopus oocytes expressing O. coarctata or rice HKT1;5 transporters indicates that OcHKT1;5, like OsHKT1;5-Ni is a Na+-selective transporter, but displays 16-fold lower affinity for Na+ and 3.5-fold higher maximal conductance than OsHKT1;5-Ni. For Na+ concentrations greater than 10 mM, OcHKT1;5 conductance is higher than that of OsHKT1;5-Ni, indicating potential of OcHKT1;5 for increasing domesticated rice salt tolerance. Homology modeling/ simulation suggests that four key amino acid changes in OcHKT1;5 (in loops on the extracellular side; E239K, G207R, G214R, L363V), account for its lower affinity and higher Na+ conductance vis-{\`a}-vis OsHKT1;5-Ni. Of these, E239K in OcHKT1;5, confers lower affinity for Na+ transport, as evidenced by Na+ transport assays of reciprocal site directed mutants for both transporters (OcHKT1;5- K239E, OsHKT1;5-Ni- E270K) in Xenopus oocytes. Both transporters have analogous roles in xylem sap desalinization and differences in Na+ transport affinity/ conductance between the transporters is attributable to differences in xylem sap Na+ concentrations in both species.</p>
},
	issn = {1471-9053},
	doi = {10.1093/pcp/pcaa061},
	author = {Somasundaram, Suji and V{\'e}ry, Anne-Ali{\'e}nor and Vinekar, Rithvik S and Ishikawa, Tetsuya and Kumari, Kumkum and Pulipati, Shalini and Kumaresan, Kavitha and Corratg{\'e}-Faillie, Claire and Sowdhamini, R and Parida, Ajay and Shabala, Lana and Shabala, Sergey and Venkataraman, Gayatri}
}
