Whole-Genome and Expression Analyses of Bamboo Aquaporin Genes Reveal Their Functions Involved in Maintaining Diurnal Water Balance in Bamboo Shoots

A bamboo 'PeSAPK4-PeMYB99-PeTIP4-3' regulatory model involved in water transport

Water plays crucial roles in expeditious growth and osmotic stress of bamboo. Nevertheless, the molecular mechanism of water transport remains unclear. In this study, an aquaporin gene, PeTIP4-3, was identified through a joint analysis of root pressure and transcriptomic data in moso bamboo (Phyllostachys edulis). PeTIP4-3 was highly expressed in shoots, especially in the vascular bundle sheath cells. Overexpression of PeTIP4-3 could increase drought and salt tolerance in transgenic yeast and rice. A co-expression pattern of PeSAPK4, PeMYB99 and PeTIP4-3 was revealed by WGCNA. PeMYB99 exhibited an ability to independently bind to and activate PeTIP4-3, which augmented tolerance to drought and salt stress. PeSAPK4 could interact with and phosphorylate PeMYB99 in vivo and in vitro, wherein they synergistically accelerated PeTIP4-3 transcription. Overexpression of PeMYB99 and PeSAPK4 also conferred drought and salt tolerance in transgenic rice. Further ABA treatment analysis indicated that PeSAPK4 enhanced water transport in response to stress via ABA signaling. Collectively, an ABA-mediated cascade of PeSAPK4-PeMYB99-PeTIP4-3 is proposed, which governs water transport in moso bamboo.

Positive pressure in bamboo is generated in stems and rhizomes, not in roots

Bamboos stand out among other tall plants in being able to generate positive pressure in the xylem at night, pushing water up to the leaves and causing drops to fall from leaf tips as guttation that can amount to a steady nocturnal 'bamboo rain'. The location and mechanism of nocturnal pressure generation in bamboos are unknown, as are the benefits for the plants. We conducted a study on the tall tropical bamboo species Bambusa oldhamii (giant timber bamboo) growing outdoors in southern California under full irrigation to determine where in the plant the nocturnal pressure is generated, when it rises in the evening, and when it dissipates in the morning. We hypothesized that the build-up of positive pressure would be triggered by the cessation of transpiration-driven sap flow and that resumption of sap flow in the morning would cause the pressure to dissipate. Nocturnal pressure was observed in mature stems and rhizomes, but never in roots. The pressure was episodic and associated with stem swelling and was usually, but not always, higher in rhizomes and basal stems than in stems at greater height. Time series analyses revealed that dry atmospheric conditions were followed by lower nocturnal pressure and rainfall events by higher stem pressure. Nocturnal pressure was unrelated to sap flow and even was generated for a short time in isolated stem pieces placed in water. We conclude that nocturnal pressure in bamboo is not 'root pressure' but is generated in the pseudo-woody rhizomes and stems. It is unrelated to the presence or absence of sap flow and therefore must be created outside of vessels, such as in phloem, parenchyma, or fibres. It is unlikely to be a drought adaptation and may benefit the plants by maximizing stem water storage for daytime transpiration or by transporting nutrients to the leaves.

Searching for mechanisms driving root pressure in Zea mays-a transcriptomic approach

While there are many theories and a variety of innovative datasets contributing to our understanding of the mechanism generating root pressure in vascular plants, we are still unable to produce a specific cellular mechanism for any species. To discover these mechanisms, we used RNA-Seq to explore differentially expressed genes in three different tissues between individual Zea mays plants expressing root pressure and those producing none. Working from the perspective that roots cells are utililizing a combination of osmotic exudation and hydraulic pressure mechanisms to generate positively-pressured flow of water into the xylem from the soil, we hypothesized that differential expression analysis would yield candidate genes coding for membrane transporters, ion channels, ATPases, and hormones with clear relevance to root pressure generation. In basal stem and coarse root tissue, we observed these classes of differentially expressed genes and more, including a strong cytoskeletal remodeling response. Fine roots displayed remarkably little differential expression relevant to root pressure, leading us to conclude that they either do not contribute to root pressure generation or are constitutively expressing root pressure mechanisms regardless of soil water content.

Phylogeny, transcriptional profile, and auxin-induced phosphorylation modification characteristics of conserved PIN proteins in Moso bamboo (Phyllostachys edulis)

Auxin polar transport is an important way for auxin to exercise its function, and auxin plays an irreplaceable role in the rapid growth of Moso bamboo. We identified and performed the structural analysis of PIN-FORMED auxin efflux carriers in Moso bamboo and obtained a total of 23 PhePIN genes from five gene subfamilies. We also performed chromosome localization and intra- and inter-species synthesis analysis. Phylogenetic analyses of 216 PIN genes showed that PIN genes are relatively conserved in the evolution of the Bambusoideae and have undergone intra-family segment replication in Moso bamboo. The PIN genes' transcriptional patterns showed that the PIN1 subfamily plays a major regulatory role. PIN genes and auxin biosynthesis maintain a high degree of consistency in spatial and temporal distribution. Phosphoproteomics analysis identified many phosphorylated protein kinases that respond to auxin regulation through autophosphorylation and phosphorylation of PIN proteins. The protein interaction network showed that there is a plant hormone interaction regulatory network with PIN protein as the core. We provide a comprehensive PIN protein analysis that complements the auxin regulatory pathway in Moso bamboo and paves the way for further auxin regulatory studies in bamboo.

Genome survey sequencing-based SSR marker development and their validation in Dendrocalamus longispathus

Bamboo is an important genetic resource in India, supporting rural livelihood and industries. Unfortunately, most Indian bamboo taxa are devoid of basic genomic or marker information required to comprehend the genetic processes for further conservation and management. In this study, we perform genome survey sequencing for development of de novo genomic SSRs in Dendrocalamus longispathus, a socioeconomically important bamboo species of northeast India. Using Illumina platform, 69.49 million raw reads were generated and assembled into 1,145,321 contig with GC content 43% and N50 1228 bp. In total, 46,984 microsatellite repeats were mined-out wherein di-nucleotide repeats were most abundant (54.71%) followed by mono- (31.91%) and tri-repeats (9.85%). Overall, AT-rich repeats were predominant in the genome, but GC-rich motifs were more frequent in tri-repeats. Afterwards, 21,596 SSR loci were successfully tagged with the primer pairs, and a subset of 50 were validated through polymerase chain reaction amplification. Of these, 36 SSR loci were successfully amplified, and 16 demonstrated polymorphism. Using 13 polymorphic SSRs, a moderate level of gene diversity (He = 0.480; Ar = 3.52) was recorded in the analysed populations of D. longispathus. Despite the high gene flow (Nm = 4.928) and low genetic differentiation (F_ST = 0.119), severe inbreeding (F_IS = 0.407) was detected. Further, genetic clustering and STRUCTURE analysis revealed that the entire genetic variability is captured under two major gene pools. Conclusively, we present a comprehensive set of novel SSR markers in D. longispathus as well as other taxa of tropical woody bamboos.

Overexpression of DsEXLA2 gene from Dendrocalamus sinicus accelerates the plant growth rate of Arabidopsis

Expansins play crucial roles in cell wall loosening and a range of life activities involving cell wall modification. Nevertheless, the biological functions of expansin genes during fast growth of bamboo remain unclear. In this study, Dendrocalamus sinicus, the largest and fastest growing bamboo species in the world, was used as the research material, and the full length of DsEXLA2 was cloned. Bioinformatics analysis revealed that DsEXLA2 contained expansin family typical domains (DPBB_1 and Pollen_allerg_1, CDRC motif) and amino acid sequence was highly conserved among different species. The expression level of DsEXLA2 increased from top section to basal section in different internodes. Subcellular localization verified that DsEXLA2 protein was located in the cell wall. Further genetic transformation studies in Arabidopsis indicated that compared with the wild type, DsEXLA2 overexpressed transgenic plants exhibited higher plant height, thicker stem, larger leaf, and less epidermal hair number and smaller stomatal aperture in the prophase and metaphase of growth. In addition, the cellulose content in the stem of transgenic plants was increased, and cell wall was thickened significantly. Moreover, a total of 1656 differentially expressed genes (DEGs) were identified by RNA-seq. The upregulated genes were predominantly enriched in the plant-pathogen interaction, MAPK signaling pathway-plant, plant hormone signal transduction, lipid metabolism and amino acid metabolism, while the downregulated genes were mainly enriched in energy metabolism, carbohydrate metabolism, plant hormone signal transduction and ribosome. These data implied that overexpression of DsEXLA2 gene accelerates the plant growth rate of Arabidopsis. This study is helpful to reveal the molecular mechanism of DsEXLA2 in culm growth and development of D. sinicus, and to understand the rapid growth of bamboos.

Dynamics in plant roots and shoots minimize stress, save energy and maintain water and nutrient uptake

Plants are inherently dynamic. Dynamics minimize stress while enabling plants to flexibly acquire resources. Three examples are presented for plants tolerating saline soil: transport of sodium chloride (NaCl), water and macronutrients is nonuniform along a branched root; water and NaCl redistribute between shoot and soil at night-time; and ATP for salt exclusion is much lower in thinner branch roots than main roots, quantified using a biophysical model and geometry from anatomy. Noninvasive phenotyping and precision agriculture technologies can be used together to harness plant dynamics, but analytical methods are needed. A plant advancing in time through a soil and atmosphere space is proposed as a framework for dynamic data and their relationship to crop improvement.

The Tonoplast Intrinsic Protein Gene KvTIP3 is Responsive to Different Abiotic Stresses in Kosteletzkya virginica

In higher plants, aquaporin proteins (AQPs) play important roles in the uptake of water across cell membranes. However, their functions in halophytes are still largely unknown. In this work, we isolated, cloned, and identified KvTIP3, a tonoplast intrinsic protein gene from Kosteletzkya virginica. Bioinformatic analyses demonstrated that KvTIP3 encoded a tonoplast protein with the common properties of AQPs. Further multiple sequence alignment and phylogenetic analyses showed that KvTIP3 shared 65%–82% homology with other AQPs from Arabidopsis, cotton, polar, and cocoa. Quantitative real-time PCR (qPCR) analyses revealed that KvTIP3 was ubiquitously expressed in various tissues such as leaves, stems, and roots, with a predominant expression in roots. In addition, KvTIP3 transcript was strongly induced by NaCl, low temperature, and ABA in K. virginica. Our findings suggest that KvTIP3 encodes a new AQP possibly involved in multiple abiotic stress responses in K. virginica, and KvTIP3 could be used as a potential candidate gene for the improvement of plants resistant to various abiotic stresses.

Genome-Wide Characterization and Gene Expression Analyses of GATA Transcription Factors in Moso Bamboo (Phyllostachys edulis)

Moso bamboo is well-known for its rapid-growth shoots and widespread rhizomes. However, the regulatory genes of these two processes are largely unexplored. GATA transcription factors regulate many developmental processes, but their roles in moso bamboo height control and rhizome development remains unexplored. Here, thirty-one bamboo GATA factors (PeGATAs) were identified, which are evolutionarily closer to rice than Arabidopsis, and their gene expression patterns were analyzed in bamboo development and phytohormone response with bioinformatics and molecular methods. Interestingly, PeGATAs could only be classified into three groups. Phytohormone responsive cis-elements were found in PeGATA promoters and the expression profiles showed that PeGATA genes might respond to gibberellin acid and abscisic acid but not to auxin at the transcriptional level. Furthermore, PeGATA genes have a tissue-specific expression pattern in bamboo rhizomes. Interestingly, most PeGATA genes were down-regulated during the rapid-growth of bamboo shoots. In addition, over-expressing one of the PeGATA genes, PeGATA26, significantly repressed the primary root length and plant height of transgenic Arabidopsis plants, which may be achieved by promoting the gibberellin acid turnover. Overall, our results provide insight into the function of GATA transcription factors in bamboo, and into genetic resources for engineering plant height.

Genome-wide identification and expression analysis of aquaporin gene family related to abiotic stress in watermelon

The plant aquaporins (AQPs) are highly conserved integral membrane proteins that participate in multiple developmental processes and responses to various stresses. In this study, a total of 35 AQP genes were identified in the watermelon genome. The phylogenetic analysis showed that these AQPs can be divided into five types, including 16 plasma membrane intrinsic proteins (PIPs), eight tonoplast intrinsic proteins (TIPs), eight nodulin 26-like intrinsic proteins (NIPs), two small basic intrinsic proteins (SIPs), and one uncategorized X intrinsic protein (XIP). A number of cis-elements related to plant responses to hormones and stresses were detected in the promoter sequences of ClAQP genes. Chromosome distribution analysis revealed that the genes are unevenly distributed on eight chromosomes, with chromosomes 1 and 4 possessing the most genes. Expression analysis at different developmental stages in flesh and rind indicated that most of ClAQPs have tissue-specific expression. Meanwhile, some other AQP genes showed differential expression in response to cold, salt, and ABA treatments, which is consistent with the organization of the stress-responsive cis-elements detected in the promoter regions. Our results lay a foundation for understanding the specific functions of ClAQP genes to help the genetic improvement of watermelon.

Exploring the Roles of Aquaporins in Plant⁻Microbe Interactions

Aquaporins (AQPs) are membrane channel proteins regulating the flux of water and other various small solutes across membranes. Significant progress has been made in understanding the roles of AQPs in plants' physiological processes, and now their activities in various plant⁻microbe interactions are receiving more attention. This review summarizes the various roles of different AQPs during interactions with microbes which have positive and negative consequences on the host plants. In positive plant⁻microbe interactions involving rhizobia, arbuscular mycorrhizae (AM), and plant growth-promoting rhizobacteria (PGPR), AQPs play important roles in nitrogen fixation, nutrient transport, improving water status, and increasing abiotic stress tolerance. For negative interactions resulting in pathogenesis, AQPs help plants resist infections by preventing pathogen ingress by influencing stomata opening and influencing defensive signaling pathways, especially through regulating systemic acquired resistance. Interactions with bacterial or viral pathogens can be directly perturbed through direct interaction of AQPs with harpins or replicase. However, whilst these observations indicate the importance of AQPs, further work is needed to develop a fuller mechanistic understanding of their functions.