In-silico Exploration of Channel Type and Efflux Silicon Transporters and Silicification Proteins in 80 Sequenced Viridiplantae Genomes

Abstract

Silicon (Si) accumulation protects plants from biotic and abiotic stresses. It is transported and distributed within the plant body through a cooperative system of channel type (e.g., OsLsi1) and efflux (Lsi2s e.g., OsLsi2) Si transporters (SITs) that belong to Noduline-26 like intrinsic protein family of aquaporins and an uncharacterized anion transporter family, respectively. Si is deposited in plant tissues as phytoliths and the process is known as biosilicification but the knowledge about the proteins involved in this process is limited. In the present study, we explored channel type SITs and Lsi2s, and siliplant1 protein (Slp1) in 80 green plant species. We found 80 channel type SITs and 133 Lsi2s. The channel type SITs characterized by the presence of two NPA motifs, GSGR or STAR selectivity filter, and 108 amino acids between two NPA motifs were absent from Chlorophytes, while Streptophytes evolved two different types of channel type SITs with different selectivity filters. Both channel type SITs and Lsi2s evolved two types of gene structures each, however, Lsi2s are ancient and were also found in Chlorophyta. Homologs of Slp1 (225) were present in almost all Streptophytes regardless of their Si accumulation capacity. In Si accumulator plant species, the Slp1s were characterized by the presence of H, D-rich domain, P, K, E-rich domain, and P, T, Y-rich domain, while moderate Si accumulators lacked H, D-rich domain and P, T, Y-rich domains. The digital expression analysis and coexpression networks highlighted the role of channel type and Lsi2s, and how Slp1 homologs were ameliorating plants’ ability to withstand different stresses by co-expressing with genes related to structural integrity and signaling. Together, the in-silico exploration made in this study increases our knowledge of the process of biosilicification in plants.

Genome-wide identification and functional prediction of silicon (Si) transporters in poplar (Populus trichocarpa)

“…Previous studies found that the Lsi2 protein in plants is localized in the plasma membrane, featuring 9-11 TMDs, with extracellular N-and extracellular/cytoplasmic C-terminus regions (Vivancos et al 2016;Vatansever et al 2017;Nawaz et al 2020). Similarly, we identified 9-11 TMDs in the putative poplar Lsi2 homologs except Potri.017G141950.1, which contained five TMDs (Supplementary Fig.…”

“…Similar to OsLsi1/OsLsi6, the distance between the two NPA motifs in PtLsi1 is 108 AA. The channel-type SITs in plants have six transmembrane domains (TMDs) (Wallace and Roberts 2004;Ma et al 2006;Nawaz et al 2020). We also found six TMDs in PtLsi1 (Fig.…”

“…1), further supporting the notion that this gene is the putative poplar Lsi2 homolog corresponding to OsLsi2. A recent study (Nawaz et al 2020) identified a highly conserved region with a consensus sequence "XXTKHXWFXXCXXXXRX" among the Lsi2 proteins in different plant species such as rice, wheat, and Sorghum. This conserved sequence, however, was not found in the Lsi2 homologs in poplar.…”

“…Out of the 27 proteins, there were only two poplar proteins which will be referred to as PtSlp1a (Potri.004G168600.10) and PtSlp1b (Potri.009G129900.6) in the remaining text. The isoelectric point (pI value) of these proteins was computed as positively charged AAs are involved in biosilicification (Otzen 2012;Nawaz et al 2020;Kumar et al 2020). The predicted pI values of the poplar Slp1 homologs were 9.96 and 9.78 (Table 1) for PtSlp1a and Ptslp1b, respectively.…”

“…The uptake, transport and deposition of Si from soil to a plant is mediated by a cooperative action of various transporter genes, such as channel-type influx (e.g., Lsi1/Lsi6) and efflux (e.g., Lsi2) transporters (Kaur and Greger 2019;Nawaz et al 2020). The first Si transporter gene identified in plants was rice (Oryza sativa L.) low silicon 1 (OsLsi1) (Ma et al 2006).…”