Genome-wide identification of the pectate lyase-like (PLL) gene family and functional analysis of two PLL genes in rice

Mol Genet Genomics. 2018 Dec;293(6):1317-1331. doi: 10.1007/s00438-018-1466-x. Epub 2018 Jun 25.


Pectate lyase catalyses the eliminative cleavage of de-esterified pectin, which is a major component of primary cell walls in many higher plants. Pectate lyase-like (PLL) genes have been identified in various plant species and are involved in a broad range of physiological processes associated with pectin degradation. Previous studies have functionally identified two PLL genes in rice (Oryza sativa. L). However, the knowledge concerning genome-wide analysis of this family remains limited, and functions of the other PLL genes have not been thoroughly elucidated to date. In this study, we identified 12 PLL genes based on a genome-wide investigation in rice. A complete overview of this gene family is presented, including chromosomal locations, exon-intron structure, cis-acting elements and conserved motifs. PLL protein sequences from multiple plant species were compared and divided into five groups based on phylogenetic analysis. Quantitative RT-PCR analysis revealed that only a portion of OsPLL genes (4 of 12) exhibits detectable expression levels. Notably, OsPLL1, OsPLL3, OsPLL4 and OsPLL12 exhibit strong and preferential expression in panicles suggesting that the potential roles of these genes are crucial during rice panicle development. Moreover, knockdown of OsPLL3 and OsPLL4 by artificial microRNA (amiRNA) disrupted normal pollen development and resulted in partial male sterility. These results could provide valuable information for characterising the functions and dissecting the molecular mechanisms of the OsPLL genes.

Keywords: Expression analysis; Pectate lyase; Phylogenetic analysis; Rice; amiRNA.

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • Chromosome Mapping
  • Gene Expression Profiling
  • Gene Expression Regulation, Plant
  • Genome, Plant
  • Multigene Family
  • Oryza / enzymology
  • Oryza / genetics*
  • Phylogeny
  • Plant Proteins / genetics
  • Plant Proteins / physiology
  • Plants, Genetically Modified
  • Polysaccharide-Lyases / genetics*
  • Polysaccharide-Lyases / physiology*


  • Plant Proteins
  • Polysaccharide-Lyases
  • pectate lyase