Regulated expression of a calmodulin isoform alters growth and development in potato

Calmodulin and calcium signaling in potato tuberization: The role of membrane transporters in stress adaptation

Potato tuberization is a complex developmental process influenced by environmental factors, such as light and temperature, as well as genetic and biochemical factors. Tuber formation is responsive to day length, with shorter days inducing tuberization more effectively than longer days. Potato tuber yield is regulated by signaling networks involving hormones, transcriptional regulators, and sugars. Calcium plays a pivotal role in this process. Elevated cytoplasmic calcium is detected by calcium sensors, including calmodulins (CaMs), calmodulin-like proteins (CMLs), Ca2+-dependent protein kinases (CDPKs), and calcineurin-B-like proteins (CBLs), promoting tuberization and growth. This review provides mechanistic insights into calcium signaling in potato tuberization, emphasizing its role in stress adaptation. This review further explores the role of calcium/calmodulin in stress response mechanisms and the membrane transporters that facilitate adaptation to environmental challenges like drought, cold, flooding, and heat stress, which are significant threats to potato production globally. Additionally, calcium signaling helps develop tolerance to both abiotic stresses and pathogens, ultimately enhancing plant immune responses to protect potato tubers.

Elucidation of the interactome of the sucrose transporter StSUT4: sucrose transport is connected to ethylene and calcium signalling

Sucrose transporters of the SUT4 clade show dual targeting to both the plasma membrane as well as to the vacuole. Previous investigations revealed a role for the potato sucrose transporter StSUT4 in flowering, tuberization, shade avoidance response, and ethylene production. Down-regulation of StSUT4 expression leads to early flowering, tuberization under long days, far-red light insensitivity, and reduced diurnal ethylene production. Sucrose export from leaves was increased and a phase-shift of soluble sugar accumulation in source leaves was observed, arguing for StSUT4 to be involved in the entrainment of the circadian clock. Here, we show that StSUT4, whose transcripts are highly unstable and tightly controlled at the post-transcriptional level, connects components of the ethylene and calcium signalling pathway. Elucidation of the StSUT4 interactome using the split ubiquitin system helped to prove direct physical interaction between the sucrose transporter and the ethylene receptor ETR2, as well as with the calcium binding potato calmodulin-1 (PCM1) protein, and a calcium-load activated calcium channel. The impact of calcium ions on transport activity and dual targeting of the transporter was investigated in detail. For this purpose, a reliable esculin-based transport assay was established for SUT4-like transporters. Site-directed mutagenesis helped to identify a diacidic motif within the seventh transmembrane spanning domain that is essential for sucrose transport activity and targeting, but not required for calcium-dependent inhibition. A link between sucrose, calcium and ethylene signalling has been previously postulated with respect to pollen tube growth, shade avoidance response, or entrainment of the circadian clock. Here, we provide experimental evidence for the direct interconnection of these signalling pathways at the molecular level by direct physical interaction of the main players.

Transcriptome Analysis of Gene Expression during Chinese Water Chestnut Storage Organ Formation

The product organ (storage organ; corm) of the Chinese water chestnut has become a very popular food in Asian countries because of its unique nutritional value. Corm formation is a complex biological process, and extensive whole genome analysis of transcripts during corm development has not been carried out. In this study, four corm libraries at different developmental stages were constructed, and gene expression was identified using a high-throughput tag sequencing technique. Approximately 4.9 million tags were sequenced, and 4,371,386, 4,372,602, 4,782,494, and 5,276,540 clean tags, including 119,676, 110,701, 100,089, and 101,239 distinct tags, respectively, were obtained after removal of low-quality tags from each library. More than 39% of the distinct tags were unambiguous and could be mapped to reference genes, while 40% were unambiguous tag-mapped genes. After mapping their functions in existing databases, a total of 11,592, 10,949, 10,585, and 7,111 genes were annotated from the B1, B2, B3, and B4 libraries, respectively. Analysis of the differentially expressed genes (DEGs) in B1/B2, B2/B3, and B3/B4 libraries showed that most of the DEGs at the B1/B2 stages were involved in carbohydrate and hormone metabolism, while the majority of DEGs were involved in energy metabolism and carbohydrate metabolism at the B2/B3 and B3/B4 stages. All of the upregulated transcription factors and 9 important genes related to product organ formation in the above four stages were also identified. The expression changes of nine of the identified DEGs were validated using a quantitative PCR approach. This study provides a comprehensive understanding of gene expression during corm formation in the Chinese water chestnut.

Genome-Wide Analysis of Differentially Expressed Genes Relevant to Rhizome Formation in Lotus Root (Nelumbo nucifera Gaertn)

Lotus root is a popular wetland vegetable which produces edible rhizome. At the molecular level, the regulation of rhizome formation is very complex, which has not been sufficiently addressed in research. In this study, to identify differentially expressed genes (DEGs) in lotus root, four libraries (L1 library: stolon stage, L2 library: initial swelling stage, L3 library: middle swelling stage, L4: later swelling stage) were constructed from the rhizome development stages. High-throughput tag-sequencing technique was used which is based on Solexa Genome Analyzer Platform. Approximately 5.0 million tags were sequenced, and 4542104, 4474755, 4777919, and 4750348 clean tags including 151282, 137476, 215872, and 166005 distinct tags were obtained after removal of low quality tags from each library respectively. More than 43% distinct tags were unambiguous tags mapping to the reference genes, and 40% were unambiguous tag-mapped genes. From L1, L2, L3, and L4, total 20471, 18785, 23448, and 21778 genes were annotated, after mapping their functions in existing databases. Profiling of gene expression in L1/L2, L2/L3, and L3/L4 libraries were different among most of the selected 20 DEGs. Most of the DEGs in L1/L2 libraries were relevant to fiber development and stress response, while in L2/L3 and L3/L4 libraries, major of the DEGs were involved in metabolism of energy and storage. All up-regulated transcriptional factors in four libraries and 14 important rhizome formation-related genes in four libraries were also identified. In addition, the expression of 9 genes from identified DEGs was performed by qRT-PCR method. In a summary, this study provides a comprehensive understanding of gene expression during the rhizome formation in lotus root.

Identification of differentially expressed genes relevant to corm formation in Sagittaria trifolia

Sagittaria trifolia is a good model of wetland plants to elucidate the formation of corm. However, few studies have been conducted to uncover the complexity of gene expression involved in corm formation. In this study, high-throughput tag-sequencing based on Solexa Genome Analyzer Platform was applied to monitor the changes in gene expression with three libraries of differentially expressed genes (DEGs) (C1 library: stolon stage, C2 library: initial swelling stage and C3 library: swelling stage) during corm formation in Sagittaria trifolia. Approximately 6.0 million tags were sequenced, and 5854021, 5983454, and 5761079 clean tags including 138319, 116804, and 101739 distinct tags were obtained after removal of low quality tags from each library, respectively. About 46% distinct tags were unambiguous tags mapping to the reference genes, and 33% were unambiguous tag-mapped genes. Totally, 20575, 19807, and 18438 were annotated in C1, C2, and C3 libraries, respectively, after mapping their functions in existing databases. In addition, we found that profiling of gene expression in C1/C2 and C2/C3 libraries were different among most of the selected 20 DEGs. Most DEGs in C1/C2 libraries were relevant to hormone synthesis and response; energy metabolism and stress response, while most of the genes in C2/C3 libraries were involved in carbohydrate metabolism. All up-regulated transcriptional factors and 16 important genes relevant to corm formation in three libraries were also identified. To further analyze the expression of 9 genes, from the results of tag-sequencing, qRT-PCR was applied. In summary, this study provides a comprehensive understanding of gene expression, during the formation of corm in Sagittaria trifolia.

Sweet potato calmodulin SPCAM is involved in salt stress-mediated leaf senescence, H₂O₂ elevation and senescence-associated gene expression

The sweet potato calmodulin gene, SPCAM, was previously cloned and shown to participate in ethephon-mediated leaf senescence, H₂O₂ elevation and senescence-associated gene expression. In this report, an association of SPCAM with NaCl stress is reported. Expression of SPCAM was significantly enhanced by NaCl on days 1 and 2 after salt treatment in a dose-dependent manner and drastically decreased again on the third day. Starting on day 6, salt stress also remarkably promoted leaf senescence, H₂O₂ elevation and senescence-associated gene expression in a dose-dependent manner. These salt stress-mediated effects were strongly inhibited by chlorpromazine, a calmodulin inhibitor, and the chlorpromazine-induced repression could be reversed by exogenous application of purified calmodulin fusion protein. These data suggest an involvement of calmodulin in salt stress-mediated leaf senescence, H₂O₂ elevation and senescence-associated gene expression in sweet potato. Exogenous application of SPCAM fusion protein alone, however, did not significantly accelerate leaf senescence and senescence-associated gene expression, but only showed a slight effect 12 days after treatment. These data suggest that additional components are involved in salt stress-mediated leaf senescence in sweet potato, possibly induced by and coordinated with SPCAM. In conclusion, the sweet potato calmodulin gene is NaCl-inducible and participates in salt stress-mediated leaf senescence, H₂O₂ elevation and senescence-associated gene expression.

Dynamic proteomic profile of potato tuber during its in vitro development

Potato tuberization is a complicated biochemical process, which is dependent on external environmental factors. Tuber development in potato consists of a series of biochemical and morphological processes at the stolon tip. Signal transduction proteins are involved in the source-sink transition during potato tuberization. In the present study, we examined protein profiles under in vitro tuber-inducing conditions using a shotgun proteomic approach involving denaturing gel electrophoresis and liquid chromatography-mass spectrometry. A total of 251 proteins were identified and classified into 9 groups according to distinctive expression patterns during the tuberization stage. Stolon stage-specific proteins were primarily involved in the photosynthetic machinery. Proteins specific to the initial tuber stage included patatin. Proteins specific to the developing tuber stage included 6-fructokinase, phytoalexin-deficient 4-1, metallothionein II-like protein, and malate dehydrogenase. Novel stage-specific proteins identified during in vitro tuberization were ferredoxin-NADP reductase, 34 kDa porin, aquaporin, calmodulin, ripening-regulated protein, and starch synthase. Superoxide dismutase, dehydroascorbate reductase, and catalase I were most abundantly expressed in the stolon; however, the enzyme activities of these proteins were most activated at the initial tuber. The present shotgun proteomic study provides insights into the proteins that show altered expression during in vitro potato tuberization.

Cloning and characterization of a sweet potato calmodulin SPCAM that participates in ethephon-mediated leaf senescence, H2O2 elevation and senescence-associated gene expression

In this report a full-length cDNA, SPCAM, was isolated from ethephon-treated mature leaves of sweet potato. SPCAM contained 450 nucleotides (149 amino acids) in its open reading frame, and exhibited high amino acid sequence identities (ca. 76-100%) with several plant calmodulins, including Arabidopsis, carrot, ghost needle weed, pea, potato, soybean, sweet chestnut, and tobacco. Sweet potato SPCAM also contained four putative conserved calmodulin EF-hand motifs, which responded for Ca(2+) binding and cellular signalling. Phylogenetic tree analysis showed that sweet potato SPCAM exhibited closely-related association with Arabidopsis AtCAM7, which functioned as a transcriptional regulator. Reverse transcription-polymerase chain reaction (RT-PCR) analysis showed that SPCAM gene expression was not significantly increased from L1 immature leaf to L3 mature leaf, however, was remarkably enhanced in L4 early senescent leaf, and then decreased in L5 late senescent leaf. In dark- and ethephon-treated mature leaves, SPCAM expression was significantly increased from 6 to 48h, then decreased gradually until 72h after treatment. Ethephon-mediated leaf senescence, H(2)O(2) elevation, and senescence-associated gene expression, however, was remarkably inhibited by chlorpromazine, a calmodulin inhibitor. Exogenous application of purified calmodulin SPCAM fusion protein reversed the chlorpromazine repression of ethephon-mediated leaf senescence, H(2)O(2) elevation and senescence-associated gene expression. Based on these data we conclude that sweet potato SPCAM is an ethephon-inducible calmodulin and its expression is enhanced in natural and induced senescent leaves. Calmodulin SPCAM may play a physiological role in ethephon-mediated leaf senescence, H(2)O(2) elevation and senescence-associated gene expression in sweet potato leaves.

Viewpoint: Concept of redesigning proteins by manipulating calcium/calmodulin-binding domains to engineer plants with altered traits

The importance of calcium and calcium-binding proteins such as calmodulin in plant growth and development as well as plant response to environmental stimuli has been recognised for some time. However, it is only recently that the underlying mechanisms have begun to be unravelled. A variety of intracellular calcium signatures have been observed in response to various stimuli. However, how these changes induce downstream actions and how one can manipulate these events to alter plant response is an area of major interest. Here we discuss the recent advances on three intriguing calcium/calmodulin-regulated proteins: a calcium/calmodulin-regulated metabolic enzyme (DWF1); a chimeric calcium/calmodulin-dependent protein kinase (CCaMK); and a family of calcium/calmodulin-regulated transcription factors (AtSRs or CAMTAs). These proteins play critical roles in plant growth, plant : microbe interactions and plant response to multiple environmental signals. The identification and manipulation of calcium-binding and calmodulin-binding sites in these proteins have provided direct evidence for the role of calcium-binding and calmodulin-binding to the proteins, as well as providing new ways to rebuild the proteins and engineer plants to obtain desired traits.

Antisense expression of a gene encoding a calcium-binding protein in transgenic tobacco leads to altered morphology and enhanced chlorophyll

Entamoeba histolytica contains a novel calcium-binding protein like calmodulin,which was discovered earlier,and we have reported the presence of its homologue(s)and a dependent protein kinase in plants.To understand the functions of these in plants,a cDNA encoding a calcium-binding protein isolated from Entamoeba histolytica (EhCaBP)was cloned into vector pBI121 in antisense orientation and transgenic tobacco plants were raised.These plants showed variation in several phenotypic characters,of which two distinct features,more greenness and leaf thickness,were inherited in subsequent generations.The increase in the level of total chlorophyll in different plants ranged from 60% to 70%.There was no major change in chloroplast structure and in the protein level of D1,D2,LHCP and RuBP carboxylase.These morphological changes were not seen in antisense calmodulin transgenic tobacco plants,nor was the calmodulin level altered in EhCaBP antisense plants.

Ca2+/calmodulin is critical for brassinosteroid biosynthesis and plant growth

Brassinosteroids are plant-specific steroid hormones that have an important role in coupling environmental factors, especially light, with plant growth and development. How the endogenous brassinosteroids change in response to environmental stimuli is largely unknown. Ca2+/calmodulin has an essential role in sensing and transducing environmental stimuli. Arabidopsis DWARF1 (DWF1) is responsible for an early step in brassinosteroid biosynthesis that converts 24-methylenecholesterol to campesterol. Here we show that DWF1 is a Ca2+/calmodulin-binding protein and this binding is critical for its function. Molecular genetic analysis using site-directed and deletion mutants revealed that loss of calmodulin binding completely abolished the function of DWF1 in planta, whereas partial loss of calmodulin binding resulted in a partial dwarf phenotype in complementation studies. These results provide direct proof that Ca2+/calmodulin-mediated signalling has a critical role in controlling the function of DWF1. Furthermore, we observed that DWF1 orthologues from other plants have a similar Ca2+/calmodulin-binding domain, implying that Ca2+/calmodulin regulation of DWF1 and its homologues is common in plants. These results raise the possibility of producing size-engineered crops by altering the Ca2+/calmodulin-binding property of their DWF1 orthologues.

Pathogen- and NaCl-induced expression of the SCaM-4 promoter is mediated in part by a GT-1 box that interacts with a GT-1-like transcription factor

The Ca(2+)-binding protein calmodulin mediates cellular Ca(2+) signals in response to a wide array of stimuli in higher eukaryotes. Plants express numerous CaM isoforms. Transcription of one soybean (Glycine max) CaM isoform, SCaM-4, is dramatically induced within 30 min of pathogen or NaCl stresses. To characterize the cis-acting element(s) of this gene, we isolated an approximately 2-kb promoter sequence of the gene. Deletion analysis of the promoter revealed that a 130-bp region located between nucleotide positions -858 and -728 is required for the stressors to induce expression of SCaM-4. A hexameric DNA sequence within this region, GAAAAA (GT-1 cis-element), was identified as a core cis-acting element for the induction of the SCaM-4 gene. The GT-1 cis-element interacts with an Arabidopsis GT-1-like transcription factor, AtGT-3b, in vitro and in a yeast selection system. Transcription of AtGT-3b is also rapidly induced within 30 min after pathogen and NaCl treatment. These results suggest that an interaction between a GT-1 cis-element and a GT-1-like transcription factor plays a role in pathogen- and salt-induced SCaM-4 gene expression in both soybean and Arabidopsis.

Decoding Ca2+ signals in plants

Different input signals create their own characteristic Ca2+ fingerprints. These fingerprints are distinguished by frequency, amplitude, duration, and number of Ca2+ oscillations. Ca(2+)-binding proteins and protein kinases decode these complex Ca2+ fingerprints through conformational coupling and covalent modifications of proteins. This decoding of signals can lead to a physiological response with or without changes in gene expression. In plants, Ca(2+)-dependent protein kinases and Ca2+/calmodulin-dependent protein kinases are involved in decoding Ca2+ signals into phosphorylation signals. This review summarizes the elements of conformational coupling and molecular mechanisms of regulation of the two groups of protein kinases by Ca2+ and Ca2+/calmodulin in plants.

Characterization of a novel plant PP2C-like protein Ser/Thr phosphatase as a calmodulin-binding protein

Protein phosphatases regulated by calmodulin (CaM) mediate the action of intracellular Ca2+ and modulate functions of various target proteins by dephosphorylation. In plants, however, the role of Ca2+ in the regulation of protein dephosphorylation is not well understood due to a lack of information on characteristics of CaM-regulated protein phosphatases. Screening of a cDNA library of the moss Physcomitrella patens by using 35S-labeled calmodulin as a ligand resulted in identification of a gene, PCaMPP, that encodes a protein serine/threonine phosphatase with 373 amino acids. PCaMPP had a catalytic domain with sequence similarity to type 2C protein phosphatases (PP2Cs) with six conserved metal-associating amino acid residues and also had an extra C-terminal domain. Recombinant GST fusion proteins of PCaMPP exhibited Mn2+-dependent phosphatase activity, and the activity was inhibited by pyrophosphate and 1 mm Ca2+ but not by okadaic acid, orthovanadate, or beta-glycerophosphate. Furthermore, the PCaMPP activity was increased 1.7-fold by addition of CaM at nanomolar concentrations. CaM binding assays using deletion proteins and a synthetic peptide revealed that the CaM-binding region resides within the basic amphiphilic amino acid region 324-346 in the C-terminal domain. The CaM-binding region had sequence similarity to amino acids in one of three alpha-helices in the C-terminal domain of human PP2Calpha, suggesting a novel role of the C-terminal domains for the phosphatase activity. These results provide the first evidence showing possible regulation of PP2C-related phosphatases by Ca2+/CaM in plants. Genes similar to PCaMPP were found in genomes of various higher plant species, suggesting that PCaMPP-type protein phosphatases are conserved in land plants.

Identification of calmodulin isoform-specific binding peptides from a phage-displayed random 22-mer peptide library

Plants express numerous calmodulin (CaM) isoforms that exhibit differential activation or inhibition of CaM-dependent enzymes in vitro; however, their specificities toward target enzyme/protein binding are uncertain. A random peptide library displaying a 22-mer peptide on a bacteriophage surface was constructed to screen peptides that specifically bind to plant CaM isoforms (soybean calmodulin (ScaM)-1 and SCaM-4 were used in this study) in a Ca2+-dependent manner. The deduced amino acid sequence analyses of the respective 80 phage clones that were independently isolated via affinity panning revealed that SCaM isoforms require distinct amino acid sequences for optimal binding. SCaM-1-binding peptides conform to a 1-5-10 ((FILVW)XXX(FILV) XXXX(FILVW)) motif (where X denotes any amino acid), whereas SCaM-4-binding peptide sequences conform to a 1-8-14 ((FILVW)XXXXXX(FAILVW)XXXXX(FILVW)) motif. These motifs are classified based on the positions of conserved hydrophobic residues. To examine their binding properties further, two representative peptides from each of the SCaM isoform-binding sequences were synthesized and analyzed via gel mobility shift assays, Trp fluorescent spectra analyses, and phosphodiesterase competitive inhibition experiments. The results of these studies suggest that SCaM isoforms possess different binding sequences for optimal target interaction, which therefore may provide a molecular basis for CaM isoform-specific function in plants. Furthermore, the isolated peptide sequences may serve not only as useful CaM-binding sequence references but also as potential reagents for studying CaM isoform-specific function in vivo.

Isolation and characterization of a novel calmodulin-binding protein from potato

Tuberization in potato is controlled by hormonal and environmental signals. Ca(2+), an important intracellular messenger, and calmodulin (CaM), one of the primary Ca(2+) sensors, have been implicated in controlling diverse cellular processes in plants including tuberization. The regulation of cellular processes by CaM involves its interaction with other proteins. To understand the role of Ca(2+)/CaM in tuberization, we have screened an expression library prepared from developing tubers with biotinylated CaM. This screening resulted in isolation of a cDNA encoding a novel CaM-binding protein (potato calmodulin-binding protein (PCBP)). Ca(2+)-dependent binding of the cDNA-encoded protein to CaM is confirmed by (35)S-labeled CaM. The full-length cDNA is 5 kb long and encodes a protein of 1309 amino acids. The deduced amino acid sequence showed significant similarity with a hypothetical protein from another plant, Arabidopsis. However, no homologs of PCBP are found in nonplant systems, suggesting that it is likely to be specific to plants. Using truncated versions of the protein and a synthetic peptide in CaM binding assays we mapped the CaM-binding region to a 20-amino acid stretch (residues 1216-1237). The bacterially expressed protein containing the CaM-binding domain interacted with three CaM isoforms (CaM2, CaM4, and CaM6). PCBP is encoded by a single gene and is expressed differentially in the tissues tested. The expression of CaM, PCBP, and another CaM-binding protein is similar in different tissues and organs. The predicted protein contained seven putative nuclear localization signals and several strong PEST motifs. Fusion of the N-terminal region of the protein containing six of the seven nuclear localization signals to the reporter gene beta-glucuronidase targeted the reporter gene to the nucleus, suggesting a nuclear role for PCBP.

Phytotoxic compounds from the new coprophilous fungus guanomyces polythrix

Bioactivity-directed fractionation of the fermentation broth and mycelium of the coprophilous fungus Guanomyces polythrix led to the isolation of several phytotoxic compounds, including five new naphthopyranone derivatives (1-5). In addition, rubrofusarin B, emodin, citrinin, and 4-hydroxybenzoic acid methyl ester were obtained. The structures of the new compounds were established by spectral and chiroptical methods. The isolates caused significant inhibition of radicle growth of two weed seedlings (Amaranthus hypochondriacus and Echinochloa crusgalli) and interacted with both spinach and bovine brain calmodulins.

Reciprocal regulation of mammalian nitric oxide synthase and calcineurin by plant calmodulin isoforms

Calmodulin (CaM) is the primary mediator of Ca signal transduction processes in cells. Unlike animal cells, plant cells express multiple CaM isoforms. One cloned soybean CaM isoform (SCaM-4) half-maximally activated mammalian nitric oxide synthase (NOS) at 180 nM while another (SCaM-1) served as a competitive antagonist (Ki approximately 120 nM) of this activation. The reciprocal was true for the protein phosphatase calcineurin (CaN); SCaM-1 half-maximally activated mammalian CaN at approximately 12 nM, and SCaM-4 competitively antagonized (Ki approximately 70 nM) its activation. The reciprocal enzyme activation and competitive inhibition exhibited by these plant CaM isoforms suggest that their differential expression in cells could allow selective activation of some target enzymes and the selective inhibition of others. This may allow for a branching or bifurcation in the Ca2+-CaM signal transduction pathway and to alterations in cell function.

CALMODULIN AND CALMODULIN-BINDING PROTEINS IN PLANTS

Calmodulin is a small Ca2+-binding protein that acts to transduce second messenger signals into a wide array of cellular responses. Plant calmodulins share many structural and functional features with their homologs from animals and yeast, but the expression of multiple protein isoforms appears to be a distinctive feature of higher plants. Calmodulin acts by binding to short peptide sequences within target proteins, thereby inducing structural changes, which alters their activities in response to changes in intracellular Ca2+ concentration. The spectrum of plant calmodulin-binding proteins shares some overlap with that found in animals, but a growing number of calmodulin-regulated proteins in plants appear to be unique. Ca2+-binding and enzymatic activation properties of calmodulin are discussed emphasizing the functional linkages between these processes and the diverse pathways that are dependent on Ca2+ signaling.