Genomic analysis of the polyamine biosynthesis pathway in duckweed Spirodela polyrhiza L.: presence of the arginine decarboxylase pathway, absence of the ornithine decarboxylase pathway, and response to abiotic stresses

Abstract

Main conclusion Identification of the polyamine biosynthetic pathway genes in duckweed S. polyrhiza reveals presence of prokaryotic as well as land plant-type ADC pathway but absence of ODC encoding genes. Their differential gene expression and transcript abundance is shown modulated by exogenous methyl jasmonate, salinity, and acidic pH. Abstract Genetic components encoding for polyamine (PA) biosynthetic pathway are known in several land plant species; however, little is known about them in aquatic plants. We utilized recently sequenced three duckweed (Spirodela polyrhiza) genome assemblies to map PA biosynthetic pathway genes in S. polyrhiza. PA biosynthesis in most higher plants except for Arabidopsis involves two pathways, via arginine decarboxylase (ADC) and ornithine decarboxylase (ODC). ADC-mediated PA biosynthetic pathway genes, namely, one arginase (SpARG1), two arginine decarboxylases (SpADC1, SpADC2), one agmatine iminohydrolase/deiminase (SpAIH), one N-carbamoyl putrescine amidase (SpCPA), three S-adenosylmethionine decarboxylases (SpSAMDc1, 2, 3), one spermidine synthase (SpSPDS1) and one spermine synthase (SpSPMS1) in S. polyrhiza genome were identified here. However, no locus was found for ODC pathway genes in this duckweed. Hidden Markov Model protein domain analysis established that SpADC1 is a prokaryotic/biodegradative type ADC and its molecular phylogenic classification fell in a separate prokaryotic origin ADC clade with SpADC2 as a biosynthetic type of arginine decarboxylase. However, thermospermine synthase (t-SPMS)/Aculis5 genes were not found present. Instead, one of the annotated SPDS may also function as SPMS, since it was found associated with the SPMS phylogenetic clade along with known SPMS genes. Moreover, we demonstrate that S. polyrhiza PA biosynthetic gene transcripts are differentially expressed in response to unfavorable conditions, such as exogenously added salt, methyl jasmonate, or acidic pH environment as well as in extreme temperature regimes. Thus, S. polyrhiza genome encodes for complete polyamine biosynthesis pathway and the genes are transcriptionally active in response to changing environmental conditions suggesting an important role of polyamines in this aquatic plant.

Male Fertility under Environmental Stress: Do Polyamines Act as Pollen Tube Growth Protectants?

“…Similar to other plant cells, the ability of pollen to withstand stressful conditions is related to its intrinsic biochemical, physiological, and cytological characteristics, for example the production of HSPs or osmoprotectants [97], as well as the fine-tuning of ROS and Ca 2+ levels and the ability to build a cell wall suitable for new conditions [98]. PAs have often been associated with the environmental stress response as they interface with various intracellular signaling processes [11,99], such as phosphorylation [100] and cation transport [8].…”

Genome-wide analysis of polyamine biosynthesis genes in wheat reveals gene expression specificity and involvement of STRE and MYB-elements in regulating polyamines under drought

“…The other involved Put biosynthesis genes through the ADC pathway; AIH and CPA / NLP1 have not been identified in too many species. In the current study, five TaAIH and two TaNPL1 were revealed by analysis, while a single AIH and NPL1 were found in S. polyrhiza [ 30 ] and Citrus as in A. thaliana [ 31 ]. Rice showed to have one AIH and four NLP1 [ 25 ].…”

“…The occurrence of different routes for Put biosynthesis through both ADC and ODC was formerly described in different species, particularly under stressors [ 10 , 24 , 29 ]. Although ODC is absent from some species like A. thaliana and Spirodela polyrhiza [ 30 , 31 ], it was identified in Oryza sativa , Citrus sp. , and Glycine max by only one locus [ 32 ], two in apple [ 33 ] and three in tomato [ 24 ].…”

Genome-wide identification of nitrate transporter genes from Spirodela polyrhiza and characterization of SpNRT1.1 function in plant development

“…The rapid growth rate of S. polyrhiza requires sufficient nutrients, including nitrogen and phosphorus, to maintain its development and normal life cycle. Many S. polyrhiza protein families have been identified such as the lipoxygenase gene family ( Upadhyay et al, 2020 ), WRKY gene family ( Zhao et al, 2021 ), and polyamine biosynthesis pathway ( Upadhyay et al, 2021 ). NRT proteins act as transporters that acquire nitrogen from the environment.…”