Genomic Identification and Comparative Expansion Analysis of the Non-Specific Lipid Transfer Protein Gene Family in Gossypium

Peptide hormones in plants

Peptide hormones are defined as small secreted polypeptide-based intercellular communication signal molecules. Such peptide hormones are encoded by nuclear genes, and often go through proteolytic processing of preproproteins and post-translational modifications. Most peptide hormones are secreted out of the cell to interact with membrane-associated receptors in neighboring cells, and subsequently activate signal transductions, leading to changes in gene expression and cellular responses. Since the discovery of the first plant peptide hormone, systemin, in tomato in 1991, putative peptide hormones have continuously been identified in different plant species, showing their importance in both short- and long-range signal transductions. The roles of peptide hormones are implicated in, but not limited to, processes such as self-incompatibility, pollination, fertilization, embryogenesis, endosperm development, stem cell regulation, plant architecture, tissue differentiation, organogenesis, dehiscence, senescence, plant-pathogen and plant-insect interactions, and stress responses. This article, collectively written by researchers in this field, aims to provide a general overview for the discoveries, functions, chemical natures, transcriptional regulations, and post-translational modifications of peptide hormones in plants. We also updated recent discoveries in receptor kinases underlying the peptide hormone sensing and down-stream signal pathways. Future prospective and challenges will also be discussed at the end of the article.

Identification and characterization of the Quinoa AP2/ERF gene family and their expression patterns in response to salt stress

The APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) transcription factors play crucial roles in plant growth, development, and responses to biotic and abiotic stresses. This study was performed to comprehensively identify and characterize the AP2/ERF gene family in quinoa (Chenopodium quinoa Willd.), a highly resilient pseudocereal crop known for its salinity tolerance. A total of 150 CqAP2/ERF genes were identified in the quinoa genome; these genes were unevenly distributed across the chromosomes. Phylogenetic analysis divided the CqAP2/ERFs into five subfamilies: 71 ERF, 49 DREB, 23 AP2, 3 RAV, and 4 Soloist. Additionally, the DREB and ERF subfamilies were subdivided into four and seven subgroups, respectively. The exon-intron structure of the putative CqAP2/ERF genes and the conserved motifs of their encoded proteins were also identified, showing general conservation within the phylogenetic subgroups. Promoter analysis revealed many cis-regulatory elements associated with light, hormones, and response mechanisms within the promoter regions of CqAP2/ERF genes. Synteny analysis revealed that segmental duplication under purifying selection pressure was the major evolutionary driver behind the expansion of the CqAP2/ERF gene family. The protein-protein interaction network predicted the pivotal CqAP2/ERF proteins and their interactions involved in the regulation of various biological processes including stress response mechanisms. The expression profiles obtained from RNA-seq and qRT-PCR data detected several salt-responsive CqAP2/ERF genes, particularly from the ERF, DREB, and RAV subfamilies, with varying up- and downregulation patterns, indicating their potential roles in salt stress responses in quinoa. Overall, this study provides insights into the structural and evolutionary features of the AP2/ERF gene family in quinoa, offering candidate genes for further analysis of their roles in salt tolerance and molecular breeding.

LIPID TRANSFER PROTEIN4 regulates cotton ceramide content and activates fiber cell elongation

Cell elongation is a fundamental process for plant growth and development. Studies have shown lipid metabolism plays important role in cell elongation; however, the related functional mechanisms remain largely unknown. Here, we report that cotton (Gossypium hirsutum) LIPID TRANSFER PROTEIN4 (GhLTP4) promotes fiber cell elongation via elevating ceramides (Cers) content and activating auxin-responsive pathways. GhLTP4 was preferentially expressed in elongating fibers. Over-expression and down-regulation of GhLTP4 led to longer and shorter fiber cells, respectively. Cers were greatly enriched in GhLTP4-overexpressing lines and decreased dramatically in GhLTP4 down-regulating lines. Moreover, auxin content and transcript levels of indole-3-acetic acid (IAA)-responsive genes were significantly increased in GhLTP4-overexpressing cotton fibers. Exogenous application of Cers promoted fiber elongation, while NPA (N-1-naphthalic acid, a polar auxin transport inhibitor) counteracted the promoting effect, suggesting that IAA functions downstream of Cers in regulating fiber elongation. Furthermore, we identified a basic helix-loop-helix transcription factor, GhbHLH105, that binds to the E-box element in the GhLTP4 promoter region and promotes the expression of GhLTP4. Suppression of GhbHLH105 in cotton reduced the transcripts level of GhLTP4, resulting in smaller cotton bolls and decreased fiber length. These results provide insights into the complex interactions between lipids and auxin-signaling pathways to promote plant cell elongation.

Identification and evolution of nsLTPs in the root nodule nitrogen fixation clade and molecular response of Frankia to AgLTP24

Non-specific lipid transfer proteins (nsLTPs) are antimicrobial peptides, involved in several plant biological processes including root nodule nitrogen fixation (RNF). Nodulating plants belonging to the RNF clade establish symbiosis with the nitrogen-fixing bacteria rhizobia (legumes symbiosis model) and Frankia (actinorhizal symbiosis model) leading to root nodule formation. nsLTPs are involved in processes active in early step of symbiosis and functional nodule in both models. In legumes, nsLTPs have been shown to regulate symbiont entry, promote root cortex infection, membrane biosynthesis, and improve symbiosis efficiency. More recently, a nsLTP, AgLTP24 has been described in the context of actinorhizal symbiosis between Alnus glutinosa and Frankia alni ACN14a. AgLTP24 is secreted at an early step of symbiosis on the deformed root hairs and targets the symbiont in the nitrogen-fixing vesicles in functional nodules. nsLTPs are involved in RNF, but their functions and evolutionary history are still largely unknown. Numerous putative nsLTPs were found up-regulated in functional nodules compared to non-infected roots in different lineages within the RNF clade. Here, results highlight that nodulating plants that are co-evolving with their nitrogen-fixing symbionts appear to have independently specialized nsLTPs for this interaction, suggesting a possible convergence of function, which opens perspectives to investigate nsLTPs functions in RNF.

Non-specific LIPID TRANSFER PROTEIN 1 enhances immunity against tobacco mosaic virus in Nicotiana benthamiana

Plant non-specific lipid transfer proteins (nsLTPs) are small, cysteine-rich proteins that play significant roles in biotic and abiotic stress responses; however, the molecular mechanism of their functions against viral infections remains unclear. In this study, we employed virus-induced gene-silencing and transgenic overexpression to functionally analyse a type-I nsLTP in Nicotiana benthamiana, NbLTP1, in the immunity response against tobacco mosaic virus (TMV). NbLTP1 was inducible by TMV infection, and its silencing increased TMV-induced oxidative damage and the production of reactive oxygen species (ROS), compromised local and systemic resistance to TMV, and inactivated the biosynthesis of salicylic acid (SA) and its downstream signaling pathway. The effects of NbLTP1-silencing were partially restored by application of exogenous SA. Overexpressing NbLTP1 activated genes related to ROS scavenging to increase cell membrane stability and maintain redox homeostasis, confirming that an early ROS burst followed by ROS suppression at the later phases of pathogenesis is essential for resistance to TMV infection. The cell-wall localization of NbLTP1 was beneficial to viral resistance. Overall, our results showed that NbLTP1 positively regulates plant immunity against viral infection through up-regulating SA biosynthesis and its downstream signaling component, NONEXPRESSOR OF PATHOGENESIS-RELATED 1 (NPR1), which in turn activates pathogenesis-related genes, and by suppressing ROS accumulation at the later phases of viral pathogenesis.

From Gene to Transcript and Peptide: A Deep Overview on Non-Specific Lipid Transfer Proteins (nsLTPs)

Non-specific lipid transfer proteins (nsLTPs) stand out among plant-specific peptide superfamilies due to their multifaceted roles in plant molecular physiology and development, including their protective functions against pathogens. These antimicrobial agents have demonstrated remarkable efficacy against bacterial and fungal pathogens. The discovery of plant-originated, cysteine-rich antimicrobial peptides such as nsLTPs has paved the way for exploring the mentioned organisms as potential biofactories for synthesizing antimicrobial compounds. Recently, nsLTPs have been the focus of a plethora of research and reviews, providing a functional overview of their potential activity. The present work compiles relevant information on nsLTP omics and evolution, and it adds meta-analysis of nsLTPs, including: (1) genome-wide mining in 12 plant genomes not studied before; (2) latest common ancestor analysis (LCA) and expansion mechanisms; (3) structural proteomics, scrutinizing nsLTPs' three-dimensional structure/physicochemical characteristics in the context of nsLTP classification; and (4) broad nsLTP spatiotemporal transcriptional analysis using soybean as a study case. Combining a critical review with original results, we aim to integrate high-quality information in a single source to clarify unexplored aspects of this important gene/peptide family.

Genome-wide identification, molecular evolution and expression analysis of the non-specific lipid transfer protein (nsLTP) family in Setaria italica

BACKGROUND

Foxtail millet (Setaria italica L.) is a millet species with high tolerance to stressful environments. Plant non-specific lipid transfer proteins (nsLTPs) are a kind of small, basic proteins involved in many biological processes. So far, the genome of S. italica has been fully sequenced, and a comprehensive understanding of the evolution and expression of the nsLTP family is still lacking in foxtail millet.

RESULTS

Forty-five nsLTP genes were identified in S. italica and clustered into 5 subfamilies except three single genes (SinsLTP38, SinsLTP7, and SinsLTP44). The proportion of SinsLTPs was different in each subfamily, and members within the same subgroup shared conserved exon-intron structures. Besides, 5 SinsLTP duplication events were investigated. Both tandem and segmental duplication contributed to nsLTP expansion in S. italica, and the duplicated SinsLTPs had mainly undergone purifying selection pressure, which suggested that the function of the duplicated SinsLTPs might not diverge much. Moreover, we identified the nsLTP members in 5 other monocots, and 41, 13, 10, 4, and 1 orthologous gene pairs were identified between S. italica and S. viridis, S. bicolor, Z. mays, O. sativa, and B. distachyon, respectively. The functional divergence within the nsLTP orthologous genes might be limited. In addition, the tissue-specific expression patterns of the SinsLTPs were investigated, and the expression profiles of the SinsLTPs in response to abiotic stress were analyzed, all the 10 selected SinsLTPs were responsive to drought, salt, and cold stress. Among the selected SinsLTPs, 2 paired duplicated genes shared almost equivalent expression profiles, suggesting that these duplicated genes might retain some essential functions during subsequent evolution.

CONCLUSIONS

The present study provided the first systematic analysis for the phylogenetic classification, conserved domain and gene structure, expansion pattern, and expression profile of the nsLTP family in S. italica. These findings could pave a way for further comparative genomic and evolution analysis of nsLTP family in foxtail millet and related monocots, and lay the foundation for the functional analysis of the nsLTPs in S. italica.

Systematic and functional analysis of non-specific lipid transfer protein family genes in sugarcane under Xanthomonas albilineans infection and salicylic acid treatment

Plant non-specific lipid transfer proteins (nsLTPs) are small basic proteins that play a significant regulatory role in a wide range of physiological processes. To date, no genome-wide survey and expression analysis of this gene family in sugarcane has been performed. In this study we identified the nsLTP gene family in Saccharum spontaneum and carried out expression profiling of nsLTPs in two sugarcane cultivars (Saccharum spp.) that have different resistance to leaf scald caused by Xanthomonas albilineans (Xa) infection. The effect of stress related to exogenous salicylic acid (SA) treatment was also examined. At a genome-wide level, S. spontaneum AP85-441 had 71 SsnsLTP genes including 66 alleles. Tandem (9 gene pairs) and segmental (36 gene pairs) duplication events contributed to SsnsLTP gene family expansion. Five SsnsLTP proteins were predicted to interact with five other proteins. Expression of ShnsLTPI.8/10/Gb.1 genes was significantly upregulated in LCP85-384 (resistant cultivar), but downregulated in ROC20 (susceptible cultivar), suggesting that these genes play a positive regulatory role in response of sugarcane to Xa infection. Conversely, ShnsLTPGa.4/Ge.3 appears to act as a negative regulator in response Xa infection. The majority (16/17) of tested genes were positively induced in LCP85-384 72 h after SA treatment. In both cultivars, but particularly in LCP85-384, ShnsLTPIV.3/VIII.1 genes were upregulated at all time-points, suggesting that the two genes might act as positive regulators under SA stress. Meanwhile, both cultivars showed downregulated ShnsLTPGb.1 gene expression, indicating its potential negative role in SA treatment responses. Notably, the ShnsLTPGb.1 gene had contrasting effects, with positive regulation of gene expression in response to Xa infection and negative regulation induced by SA stress. Together, our results provide valuable information for elucidating the function of ShnsLTP family members under two stressors and identified novel gene sources for development of sugarcane that are tolerant of environmental stimuli.

Genome-Wide Identification and Expression Analysis of nsLTP Gene Family in Rapeseed (Brassica napus) Reveals Their Critical Roles in Biotic and Abiotic Stress Responses

Non-specific lipid transfer proteins (nsLTPs) are small cysteine-rich basic proteins which play essential roles in plant growth, development and abiotic/biotic stress response. However, there is limited information about the nsLTP gene (BnLTP) family in rapeseed (Brassica napus). In this study, 283 BnLTP genes were identified in rapeseed, which were distributed randomly in 19 chromosomes of rapeseed. Phylogenetic analysis showed that BnLTP proteins were divided into seven groups. Exon/intron structure and MEME motifs both remained highly conserved in each BnLTP group. Segmental duplication and hybridization of rapeseed’s two sub-genomes mainly contributed to the expansion of the BnLTP gene family. Various potential cis-elements that respond to plant growth, development, biotic/abiotic stresses, and phytohormone signals existed in BnLTP gene promoters. Transcriptome analysis showed that BnLTP genes were expressed in various tissues/organs with different levels and were also involved in the response to heat, drought, NaCl, cold, IAA and ABA stresses, as well as the treatment of fungal pathogens (Sclerotinia sclerotiorum and Leptosphaeria maculans). The qRT-PCR assay validated the results of RNA-seq expression analysis of two top Sclerotinia-responsive BnLTP genes, BnLTP129 and BnLTP161. Moreover, batches of BnLTPs might be regulated by BnTT1 and BnbZIP67 to play roles in the development, metabolism or adaptability of the seed coat and embryo in rapeseed. This work provides an important basis for further functional study of the BnLTP genes in rapeseed quality improvement and stress resistance.

Identification, Structural, and Expression Analyses of SPX Genes in Giant Duckweed (Spirodela polyrhiza) Reveals Its Role in Response to Low Phosphorus and Nitrogen Stresses

SPX genes play important roles in the coordinated utilization of nitrogen (N) and phosphorus (P) in plants. However, a genome-wide analysis of the SPX family is still lacking. In this study, the gene structure and phylogenetic relationship of 160 SPX genes were systematically analyzed at the genome-wide level. Results revealed that SPX genes were highly conserved in plants. All SPX genes contained the conserved SPX domain containing motifs 2, 3, 4, and 8. The 160 SPX genes were divided into five clades and the SPX genes within the same clade shared a similar motif composition. P1BS cis–elements showed a high frequency in the promoter region of SPXs, indicating that SPX genes could interact with the P signal center regulatory gene Phosphate Starvation Response1 (PHR1) in response to low P stress. Other cis–elements were also involved in plant development and biotic/abiotic stress, suggesting the functional diversity of SPXs. Further studies were conducted on the interaction network of three SpSPXs, revealing that these genes could interact with important components of the P signaling network. The expression profiles showed that SpSPXs responded sensitively to N and P deficiency stresses, thus playing a key regulatory function in P and N metabolism. Furthermore, the expression of SpSPXs under P and N deficiency stresses could be affected by environmental factors such as ABA treatment, osmotic, and LT stresses. Our study suggested that SpSPXs could be good candidates for enhancing the uptake ability of Spirodela polyrhiza for P nutrients in wastewater. These findings could broaden the understanding of the evolution and biological function of the SPX family and offer a foundation to further investigate this family in plants.

Tomato Allergy: The Characterization of the Selected Allergens and Antioxidants of Tomato (Solanum lycopersicum)-A Review

Tomatoes are one of the most broadly produced and consumed crop plants. They are the source of health-promoting nutrients such as antioxidants, including ascorbic acid, polyphenols, or carotenoids. Despite the beneficial role of tomatoes in the daily diet, they have been confirmed as one of the most prevalent allergenic vegetables. Food allergies can cause many clinical symptoms, e.g., in the gastrointestinal tract, skin, and lungs, as well as anaphylactic shock. A huge amount of clinical research has been carried out to improve the understanding of the immunological mechanisms that lead to the lack of tolerance of food antigens, which can result in either immunoglobulin E (IgE)-mediated reactions or non-IgE-mediated reactions. Lifestyle and diet play an important role in triggering food allergies. Allergy to tomatoes is also linked to other allergies, such as grass pollen and latex allergy. Numerous attempts have been made to identify and characterize tomato allergens; however, the data available on the subject are not sufficient.

Genome-wide identification of nitrate transporter 2 (NRT2) gene family and functional analysis of MeNRT2.2 in cassava (Manihot esculenta Crantz)

Nitrate transporter 2 (NRT2) proteins play an important role in nitrate uptake and utilization in plants. The NRT2 family has been identified and functionally characterized in many plants. However, no systematic identification of NRT2 family members has been reported in cassava (Manihot esculenta Crantz). In this study, six MeNRT2 genes were identified from cassava genome and named as MeNRT2.1-2.6 according to their chromosomal locations. Phylogenetic tree showed that NRT2 proteins were divided into four main subgroups, which was further supported by their gene structure and conserved motifs. All six MeNRT2 genes are randomly distributed on 4 chromosomes (LG8, LG11, LG13, and LG17), two tandem duplicated genes (MeNRT2.3/MeNRT2.4) and a pair of segmental duplicated gene (MeNRT2.1/MeNRT2.2) was detected. Subsequently, expression profiles of MeNRT2 genes in eight different tissues and in response to nitrate deficient treatment were analyzed. The results showed that the MeNRT2 genes had differential expression patterns. All of MeNRT2 genes induced by nitrate deficiency, of them the MeNRT2.2 had the highest expression level after treatment. Arabidopis transformed with MeNRT2.2 gene showed higher fresh weight than wild type plants in response to N starvation, suggesting that MeNRT2.2 play important role in adapting to low nitrogen. Taken together, our results provide the reference for further analyses of the molecular functions of the MeNRT2 gene family, but also some candidate genes for developing nitrogen efficient crops.

Characterization of non-specific lipid transfer protein (nsLtp) gene families in the Brassica napus pangenome reveals abundance variation

BACKGROUND

Brassica napus is an important agricultural species, improving stress resistance was one of the main breeding goals at present. Non-specific lipid transfer proteins (nsLTPs) are small, basic proteins which are involved in some biotic or abiotic stress responses. B. napus is susceptible to a variety of fungal diseases, so identify the BnLTPs and their expression in disease responses is very important. The common reference genome of B. napus does not contain all B. napus genes because of gene presence/absence variations between individuals. Therefore, it was necessary to search for candidate BnLTP genes in the B. napus pangenome.

RESULTS

In the present study, the BnLTP genes were identified throughout the pangenome, and different BnLTP genes were presented among varieties. Totally, 246 BnLTP genes were identified and could be divided into five types (1, 2, C, D, and G). The classification, phylogenetic reconstruction, chromosome distribution, functional annotation, and gene expression were analyzed. We also identified potential cis-elements that respond to biotic and abiotic stresses in the 2 kb upstream regions of all BnLTP genes. RNA sequencing analysis showed that the BnLTP genes were involved in the response to Sclerotinia sclerotiorum infection. We identified 32 BnLTPs linked to blackleg resistance quantitative trait locus (QTL).

CONCLUSION

The identification and analysis of LTP genes in the B. napus pangenome could help to elucidate the function of BnLTP family members and provide new information for future molecular breeding in B. napus.

Genome-wide identification and expression profile under abiotic stress of the barley non-specific lipid transfer protein gene family and its Qingke Orthologues

BACKGROUND

Plant non-specific lipid transfer proteins (nsLTPs), a group of small, basic ubiquitous proteins to participate in lipid transfer, cuticle formation and stress response, are involved in the regulation of plant growth and development. To date, although the nsLTP gene family of barley (Hordeum vulgare L.) has been preliminarily identified, it is still unclear in the recently completed genome database of barley and Qingke, and its transcriptional profiling under abiotic stress has not been elucidated as well.

RESULTS

We identified 40 barley nsLTP (HvLTP) genes through a strict screening strategy based on the latest barley genome and 35 Qingke nsLTP (HtLTP) orthologues using blastp, and these LTP genes were divided into four types (1, 2, D and G). At the same time, a comprehensive analysis of the physical and chemical characteristics, homology alignment, conserved motifs, gene structure and evolution of HvLTPs and HtLTPs further supported their similar nsLTP characteristics and classification. The genomic location of HvLTPs and HtLTPs showed that these genes were unevenly distributed, and obvious HvLTP and HtLTP gene clusters were found on the 7 chromosomes including six pairs of tandem repeats and one pair of segment repeats in the barley genome, indicating that these genes may be co-evolutionary and co-regulated. A spatial expression analysis showed that most HvLTPs and HtLTPs had different tissue-specific expression patterns. Moreover, the upstream cis-element analysis of HvLTPs and HtLTPs showed that there were many different stress-related transcriptional regulatory elements, and the expression pattern of HvLTPs and HtLTPs under abiotic stress also indicated that numerous HvLTP and HtLTP genes were related to the abiotic stress response. Taken together, these results may be due to the differences in promoters rather than by genes themselves resulting in different expression patterns under abiotic stress.

CONCLUSION

Due to a stringent screening and comprehensive analysis of the nsLTP gene family in barley and Qingke and its expression profile under abiotic stress, this study can be considered a useful source for the future studies of nsLTP genes in either barley or Qingke or for comparisons of different plant species.

Genome-wide identification and molecular evolution analysis of the heat shock transcription factor (HSF) gene family in four diploid and two allopolyploid Gossypium species

Heat shock transcription factors (HSFs) can regulate plant development and stress response. The comprehensive evolutionary history of the HSF family remains elusive in cotton. In this study, each cotton species had 78 members in Gossypium barbadense and Gossypium hirsutum. The diploid species had 39 GaHSFs in Gossypium arboreum, 31 GrHSFs in Gossypium raimondii, 34 GtHSFs in Gossypium turneri, and 34 GlHSFs in Gossypium longicalyx. The HSF family in cotton can be classified into three subfamilies, with seven groups in subfamily A and five groups in subfamily B. Different groups exhibited distinct gene proportions, conserved motifs, gene structures, expansion rates, gene loss rates, and cis-regulatory elements. The paleohexaploidization event led to the expansion of the HSF family in cotton, and the gene duplication events in six Gossypium species were inherited from their common ancestor. The HSF family in diploid species had a divergent evolutionary history, whereas two cultivated tetraploids presented a highly conserved evolution of the HSF family. The HSF members in At and Dt subgenomes of the cultivated tetraploids showed a different evolution from their corresponding diploid donors. Some HSF members were regarded as key candidates for regulating cotton development and stress response. This study provided the comprehensive information on the evolutionary history of the HSF family in cotton.

Computational-approach understanding the structure-function prophecy of Fibrinolytic Protease RFEA1 from Bacillus cereus RSA1

Microbial fibrinolytic proteases are therapeutic enzymes responsible to ameliorate thrombosis, a fatal cardiac-disorder which effectuates due to excessive fibrin accumulation in blood vessels. Inadequacies such as low fibrin specificity, lethal after-effects and short life-span of available fibrinolytic enzymes stimulates an intensive hunt for novel, efficient and safe substitutes. Therefore, we herewith suggest a novel and potent fibrinolytic enzyme RFEA1 from Bacillus cereus RSA1 (MK288105). Although, attributes such as in-vitro purification, characterization and thrombolytic potential of RFEA1 were successfully accomplished in our previous study. However, it is known that structure-function traits and mode of action significantly aid to commercialization of an enzyme. Also, predicting structural model of a protein from its amino acid sequence is challenging in computational biology owing to intricacy of energy functions and inspection of vast conformational space. Our present study thus reports In-silico structural-functional analysis of RFEA1. Sequence based modelling approaches such as-Iterative threading ASSEmbly Refinement (I-TASSER), SWISS-MODEL, RaptorX and Protein Homology/analogY Recognition Engine V 2.0 (Phyre2) were employed to model three-dimensional structure of RFEA1 and the modelled RFEA1 was validated by structural analysis and verification server (SAVES v6.0). The modelled crystal structure revealed the presence of high affinity Ca1 binding site, associated with hydrogen bonds at Asp147, Leu181, Ile185 and Val187residues. RFEA1 is structurally analogous to Subtilisin E from Bacillus subtilis 168. Molecular docking analysis using PATCH DOCK and FIRE DOCK servers was performed to understand the interaction of RFEA1 with substrate fibrin. Strong RFEA1-fibrin interaction was observed with high binding affinity (-21.36 kcal/mol), indicating significant fibrinolytic activity and specificity of enzyme RFEA1. Overall, the computational research suggests that RFEA1 is a subtilisin-like serine endopeptidase with proteolytic potential, involved in thrombus hydrolysis.

Genome-Wide Identification and Expression Analysis of the β-Amylase Gene Family in Chenopodium quinoa

β-Amylase (BAM) is an important starch hydrolase, playing a role in a variety of plant growth and development processes. In this study, 22 BAM gene family members (GFMs) were identified in quinoa (Chenopodium quinoa), an ancient crop gaining modern consumer acceptance because of its nutritional qualities. The genetic structure, phylogenetic and evolutionary relationships, and expression patterns of CqBAM GFMs in different tissues, were analyzed. Phylogenetic analyses assigned the CqBAMs, AtBAMs, and OsBAMs into four clades. The CqBAM gene family had expanded due to segmental duplication. RNA-seq analysis revealed expression of the duplicated pairs to be similar, with the expression of CqBAM GFM pairs showing a degree of tissue specificity that was confirmed by reverse transcription quantitative PCR (RT-qPCR). Several CqBAM GFMs were also responsive to abiotic stresses in shoots and/or roots. In conclusion, the BAM gene family in quinoa was identified and systematically analyzed using bioinformatics and experimental methods. These results will help to elucidate the evolutionary relationship and biological functions of the BAM gene family in quinoa.

Genome-wide identification and expression analysis of the plant specific LIM genes in Gossypium arboreum under phytohormone, salt and pathogen stress

Asiatic cotton (Gossypium arboreum) cultivated as ‘desi cotton’ in India, is renowned for its climate resilience and robustness against biotic and abiotic stresses. The genome of G. arboreum is therefore, considered as a valued reserve of information for discovering novel genes or gene functions for trait improvements in the present context of cotton cultivation world-wide. In the present study, we carried out genome-wide analysis of LIM gene family in desi cotton and identified twenty LIM domain proteins (GaLIMs) which include sixteen animals CRP-like GaLIMs and four plant specific GaLIMs with presence (GaDA1) or absence (GaDAR) of UIM (Ubiquitin Interacting Motifs). Among the sixteen CRP-like GaLIMs, eleven had two conventional LIM domains while, five had single LIM domain which was not reported in LIM gene family of the plant species studied, except in Brassica rapa. Phylogenetic analysis of these twenty GaLIM proteins in comparison with LIMs of Arabidopsis, chickpea and poplar categorized them into distinct αLIM1, βLIM1, γLIM2, δLIM2 groups in CRP-like LIMs, and GaDA1 and GaDAR in plant specific LIMs group. Domain analysis had revealed consensus [(C-X₂-C-X₁₇-H-X₂-C)-X₂-(C-X₂-C-X₁₇-C-X₂-H)] and [(C-X₂-C-X₁₇-H-X₂-C)-X₂-(C-X₄-C-X₁₅-C-X₂-H)] being conserved as first and/or second LIM domains of animal CRP-like GaLIMs, respectively. Interestingly, single LIM domain containing GaLIM15 was found to contain unique consensus with longer inter-zinc-motif spacer but shorter second zinc finger motif. All twenty GaLIMs showed variable spatio-temporal expression patterns and accordingly further categorized into distinct groups of αLIM1, βLIM1, γLIM2 δLIM2 and plant specific LIM (DA1/DAR). For the first time, response of GaDA1/DAR under the influence of biotic and abiotic stresses were studied in cotton, involving treatments with phytohormones (Jasmonic acid and Abscisic acid), salt (NaCl) and wilt causing pathogen (Fusarium oxysporum). Expressions patterns of GaDA1/DAR showed variable response and identified GaDA2 as a probable candidate gene for stress tolerance in G. arboreum.

Genome-wide survey, characterization, and expression analysis of bZIP transcription factors in Chenopodium quinoa

BACKGROUND

Chenopodium quinoa Willd. (quinoa) is a pseudocereal crop of the Amaranthaceae family and represents a promising species with the nutritional content and high tolerance to stressful environments, such as soils affected by high salinity. The basic leucine zipper (bZIP) transcription factor represents exclusively in eukaryotes and can be related to many biological processes. So far, the genomes of quinoa and 3 other Amaranthaceae crops (Spinacia oleracea, Beta vulgaris, and Amaranthus hypochondriacus) have been fully sequenced. However, information about the bZIPs in these Amaranthaceae species is limited, and genome-wide analysis of the bZIP family is lacking in quinoa.

RESULTS

We identified 94 bZIPs in quinoa (named as CqbZIP1-CqbZIP94). All the CqbZIPs were phylogenetically splitted into 12 distinct subfamilies. The proportion of CqbZIPs was different in each subfamily, and members within the same subgroup shared conserved exon-intron structures and protein motifs. Besides, 32 duplicated CqbZIP gene pairs were investigated, and the duplicated CqbZIPs had mainly undergone purifying selection pressure, which suggested that the functions of the duplicated CqbZIPs might not diverge much. Moreover, we identified the bZIP members in 3 other Amaranthaceae species, and 41, 32, and 16 orthologous gene pairs were identified between quinoa and S. oleracea, B. vulgaris, and A. hypochondriacus, respectively. Among them, most were a single copy being present in S. oleracea, B. vulgaris, and A. hypochondriacus, and two copies being present in allotetraploid quinoa. The function divergence within the bZIP orthologous genes might be limited. Additionally, 11 selected CqbZIPs had specific spatial expression patterns, and 6 of 11 CqbZIPs were up-regulated in response to salt stress. Among the selected CqbZIPs, 3 of 4 duplicated gene pairs shared similar expression patterns, suggesting that these duplicated genes might retain some essential functions during subsequent evolution.

CONCLUSIONS

The present study provided the first systematic analysis for the phylogenetic classification, motif and gene structure, expansion pattern, and expression profile of the bZIP family in quinoa. Our results would lay an important foundation for functional and evolutionary analysis of CqbZIPs, and provide promising candidate genes for further investigation in tissue specificity and their functional involvement in quinoa's resistance to salt stress.

Non-Specific Lipid Transfer Proteins in Triticum kiharae Dorof. et Migush.: Identification, Characterization and Expression Profiling in Response to Pathogens and Resistance Inducers

Non-specific lipid-transfer proteins (nsLTPs) represent a family of plant antimicrobial peptides (AMPs) implicated in diverse physiological processes. However, their role in induced resistance (IR) triggered by non-pathogenic fungal strains and their metabolites is poorly understood. In this work, using RNA-seq data and our AMP search pipeline, we analyzed the repertoire of nsLTP genes in the wheat Triticum kiharae and studied their expression in response to Fusarium oxysporum infection and treatment with the intracellular metabolites of Fusarium sambucinum FS-94. A total of 243 putative nsLTPs were identified, which were classified into five structural types and characterized. Expression analysis showed that 121 TkLTPs including sets of paralogs with identical mature peptides displayed specific expression patters in response to different treatments pointing to their diverse roles in resistance development. We speculate that upregulated nsLTP genes are involved in protection due to their antimicrobial activity or signaling functions. Furthermore, we discovered that in IR-displaying plants, a vast majority of nsLTP genes were downregulated, suggesting their role as negative regulators of immune mechanisms activated by the FS-94 elicitors. The results obtained add to our knowledge of the role of nsLTPs in IR and provide candidate molecules for genetic engineering of crops to enhance disease resistance.

Comprehensive classification of the plant non-specific lipid transfer protein superfamily towards its sequence-structure-function analysis

Background

Non-specific Lipid Transfer Proteins (nsLTPs) are widely distributed in the plant kingdom and constitute a superfamily of related proteins. Several hundreds of different nsLTP sequences—and counting—have been characterized so far, but their biological functions remain unclear. It has been clear for years that they present a certain interest for agronomic and nutritional issues. Deciphering their functions means collecting and analyzing a variety of data from gene sequence to protein structure, from cellular localization to the physiological role. As a huge and growing number of new protein sequences are available nowadays, extracting meaningful knowledge from sequence–structure–function relationships calls for the development of new tools and approaches. As nsLTPs show high evolutionary divergence, but a conserved common right handed superhelix structural fold, and as they are involved in a large number of key roles in plant development and defense, they are a stimulating case study for validating such an approach.

Methods

In this study, we comprehensively investigated 797 nsLTP protein sequences, including a phylogenetic analysis on canonical protein sequences, three-dimensional structure modeling and functional annotation using several well-established bioinformatics programs. Additionally, two integrative methodologies using original tools were developed. The first was a new method for the detection of (i) conserved amino acid residues involved in structure stabilization and (ii) residues potentially involved in ligand interaction. The second was a structure–function classification based on the evolutionary trace display method using a new tree visualization interface. We also present a new tool for visualizing phylogenetic trees.

Results

Following this new protocol, an updated classification of the nsLTP superfamily was established and a new functional hypothesis for key residues is suggested. Lastly, this work allows a better representation of the diversity of plant nsLTPs in terms of sequence, structure and function.

Genome-wide identification and expression analysis of the BURP domain-containing genes in Gossypium hirsutum

Background

Many BURP domain-containing proteins, which are unique to plants, have been identified. They performed diverse functions in plant development and the stress response. To date, only a few BURP domain-containing genes have been studied, and no comprehensive analysis of the gene family in cotton has been reported.

Results

In this study, 18, 17 and 30 putative BURP genes were identified in G. raimondii (D₅), G. arboreum (A₂) and G. hirsutum (AD₁), respectively. These BURP genes were phylogenetically classified into eight subfamilies, which were confirmed by analyses of gene structures, motifs and protein domains. The uneven distribution of BURPs in chromosomes and gene duplication analysis indicated that segmental duplication might be the main driving force of the GhBURP family expansion. Promoter regions of all GhBURPs contained at least one putative stress-related cis-elements. Analysis of transcriptomic data and qRT-PCR showed that GhBURPs showed different expression patterns in different organs, and all of them, especially the members of the RD22-like subfamily, could be induced by different stresses, such as abscisic acid (ABA) and salicylic acid (SA), which indicated that the GhBURPs may performed important functions in cotton’s responses to various abiotic stresses.

Conclusions

Our study comprehensively analyzed BURP genes in G. hirsutum, providing insight into the functions of GhBURPs in cotton development and adaptation to stresses.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5948-y) contains supplementary material, which is available to authorized users.

Genome-Wide Identification, Characterization, and Expression Analysis of the NAC Transcription Factor in Chenopodium quinoa

The NAC (NAM, ATAF, and CUC) family is one of the largest families of plant-specific transcription factors. It is involved in many plant growth and development processes, as well as abiotic/biotic stress responses. So far, little is known about the NAC family in Chenopodium quinoa. In the present study, a total of 90 NACs were identified in quinoa (named as CqNAC1-CqNAC90) and phylogenetically divided into 14 distinct subfamilies. Different subfamilies showed diversities in gene proportions, exon-intron structures, and motif compositions. In addition, 28 CqNAC duplication events were investigated, and a strong subfamily preference was found during the NAC expansion in quinoa, indicating that the duplication event was not random across NAC subfamilies during quinoa evolution. Moreover, the analysis of Ka/Ks (non-synonymous substitution rate/synonymous substitution rate) ratios suggested that the duplicated CqNACs might have mainly experienced purifying selection pressure with limited functional divergence. Additionally, 11 selected CqNACs showed significant tissue-specific expression patterns, and all the CqNACs were positively regulated in response to salt stress. The result provided evidence for selecting candidate genes for further characterization in tissue/organ specificity and their functional involvement in quinoa's strong salinity tolerance.

Genome-Wide Identification and Analysis of Class III Peroxidases in Allotetraploid Cotton (Gossypium hirsutum L.) and their Responses to PK Deficiency

Class III peroxidases (PODs), commonly known as secretable class III plant peroxidases, are plant-specific enzymes that play critical roles in not only plant growth and development but also the responses to biotic and abiotic stress. In this study, we identified 198 nonredundant POD genes, designated GhPODs, with 180 PODs being predicted to secrete into apoplast. These POD genes were divided into 10 sub-groups based on their phylogenetic relationships. We performed systematic bioinformatic analysis of the POD genes, including analysis of gene structures, phylogenetic relationships, and gene expression profiles. The GhPODs are unevenly distributed on both upland cotton sub-genome A and D chromosomes. Additionally, these genes have undergone 15 segmental and 12 tandem duplication events, indicating that both segmental and tandem duplication contributed to the expansion of the POD gene family in upland cotton. Ka/Ks analysis suggested that most duplicated GhPODs experienced negative selection, with limited functional divergence during the duplication events. High-throughput RNA-seq data indicated that most highly expressed genes might play significant roles in root, stem, leaf, and fiber development. Under K or P deficiency conditions, PODs showed different expression patterns in cotton root and leaf. This study provides useful information for further functional analysis of the POD gene family in upland cotton.

Genome-wide identification, characterization and expression analysis of the non-specific lipid transfer proteins in potato

BACKGROUND

Plant non-specific lipid transfer proteins (nsLTPs) are small, basic proteins that are abundant in higher plants. They have been reported to play an important role in various plant physiological processes, such as lipid transfer, signal transduction, and pathogen defense. To date, a comprehensive analysis of the potato nsLTP gene family is still lacking after the completion of potato (Solanum tuberosum L.) genome sequencing. A genome-wide characterization, classification and expression analysis of the StnsLTP gene family was performed in this study.

RESULTS

In this study, a total of 83 nsLTP genes were identified and categorized into eight types based on Boutrot's method. Multiple characteristics of these genes, including phylogeny, gene structures, conserved motifs, protein domains, chromosome locations, and cis-elements in the promoter sequences, were analyzed. The chromosome distribution and the collinearity analyses suggested that the expansion of the StnsLTP gene family was greatly enhanced by the tandem duplications. Ka/Ks analysis showed that 47 pairs of duplicated genes tended to undergo purifying selection during evolution. Moreover, the expression of StnsLTP genes in various tissues was analyzed by using RNA-seq data and verified by quantitative real-time PCR, revealing that the StnsLTP genes were mainly expressed in younger tissues. These results indicated that StnsLTPs may played significant and functionally varied roles in the development of different tissues.

CONCLUSION

In this study, we comprehensively analyzed nsLTPs in potato, providing valuable information to better understand the functions of StnsLTPs in different tissues and pathways, especially in response to abiotic stress.

Genome-Wide Analysis of the Zn(II)₂Cys₆ Zinc Cluster-Encoding Gene Family in Tolypocladium guangdongense and Its Light-Induced Expression

The Zn(II)₂Cys₆ zinc cluster gene family is a subclass of zinc-finger proteins, which are transcriptional regulators involved in a wide variety of biological processes in fungi. We performed genome-wide identification and characterization of Zn(II)₂Cys₆ zinc-cluster gene (C6 zinc gene) family in Tolypocladiumguangdongense, Cordycepsmilitaris and Ophiocordycepssinensis. Based on the structures of the C6 zinc domains, these proteins were observed to be evolutionarily conserved in ascomycete fungi. We focused on T.guangdongense, a medicinal fungus, and identified 139 C6 zinc genes which could be divided into three groups. Among them, 49.6% belonged to the fungal specific transcriptional factors, and 16% had a DUF3468 domain. Homologous and phylogenetic analysis indicated that 29 C6 zinc genes were possibly involved in the metabolic process, while five C6 zinc genes were supposed to be involved in asexual or sexual development. Gene expression analysis revealed that 54 C6 zinc genes were differentially expressed under light, including two genes that possibly influenced the development, and seven genes that possibly influenced the metabolic processes. This indicated that light may affect the development and metabolic processes, at least partially, through the regulation of C6 zinc genes in T.guangdongense. Our results provide comprehensive data for further analyzing the functions of the C6 zinc genes.

Identification of non-specific Lipid Transfer Protein gene family members in Solanum lycopersicum and insights into the features of Sola l 3 protein

Non-specific lipid transfer proteins (nsLTPs) are characterized by an eight-cysteine motif backbone that is stabilized by four disulphide bonds. The strong interest towards this protein family is mainly due to the fact that nsLTPs are involved in many biological processes and have been identified as major human allergens. Since tomato (Solanum lycopersicum L.) is one of the most consumed and allergenic vegetables, a full characterization of this family is needed. In this study, hidden Markov model profiles were used to identify nsLTPs within the tomato protein complement. Following manual curation, 64 nsLTP genes were classified into six sub-families. Furthermore, nsLTP gene structure, distribution and arrangement along tomato chromosomes were investigated. Available RNA-seq expression profile data and Real-Time PCR analyses were used to derive expression patterns of tomato nsLTPs in different tissues/organs. Non-specific LTP genes with high level of expression in tomato fruits were filtered out since they could play a key role in tomato allergenicity. Among these genes was Solyc10g075090 that encodes the allergen Sola l 3. Finally, cloning, heterologous expression, purification and biochemical characterization of the recombinant protein Sola l 3 was performed.

Genome-wide identification and analysis of non-specific Lipid Transfer Proteins in hexaploid wheat

Non-specific Lipid Transfer Proteins (nsLTPs) are involved in numerous biological processes. To date, only a fraction of wheat (Triticum aestivum L.) nsLTPs (TaLTPs) have been identified, and even fewer have been functionally analysed. In this study, the identification, classification, phylogenetic reconstruction, chromosome distribution, functional annotation and expression profiles of TaLTPs were analysed. 461 putative TaLTPs were identified from the wheat genome and classified into five types (1, 2, C, D and G). Phylogenetic analysis of the TaLTPs along with nsLTPs from Arabidopsis thaliana and rice, showed that all five types were shared across species, however, some type 2 TaLTPs formed wheat-specific clades. Gene duplication analysis indicated that tandem duplications contributed to the expansion of this gene family in wheat. Analysis of RNA sequencing data showed that TaLTPs were expressed in most tissues and stages of wheat development. Further, we refined the expression profile of anther-enriched expressed genes, and identified potential cis-elements regulating their expression specificity. This analysis provides a valuable resource towards elucidating the function of TaLTP family members during wheat development, aids our understanding of the evolution and expansion of the TaLTP gene family and, additionally, provides new information for developing wheat male-sterile lines with application to hybrid breeding.

Identification of Triticum aestivum nsLTPs and functional validation of two members in development and stress mitigation roles

Role of plant nsLTP in biotic stress is well reported; however, their role during abiotic stress is far from clear. This study comprises genome-wide identification of LTPs and characterizes the regulation and function of two Triticum aestivum lipid transfer proteins, TaLTP40 and TaLTP75, under stresses that influence membrane fluidity. A total of 105 LTP gene family members have been identified. The selected LTPs for functional validation were highly expressed during salt, cold and drought stress. Further, selected LTPs showed differential expression thermotolerant and thermosusceptible wheat cultivars. Higher expression of many TaLTPs was observed under different abiotic stresses in thermotolerant wheat cultivars as compared to thermosusceptible cultivars. TaLTPs regulation was correlated with light energy distribution studies under similar stress conditions. Cellular localization revealed localization of different TaLTPs to the tonoplast membrane along with the organelles involved in the secretory pathway. Induction of TaLTPs was observed upon treatment with dimethylsulphoxide. TaLTP40 and TaLTP75 overexpressing transgenic Arabidopsis showed a constitutively enhanced salt tolerance. Both the TaLTP40 and TaLTP75 overexpressing lines performed better in terms of chlorophyll a fluorescence, total chlorophyll content, membrane injury index, total biomass, percentage germination, percentage survival and relative growth rate. Hence, our analyses indicate that TaLTPs expression might be driven by change in membrane fluidity and could be involved in transferring membrane lipids to the biological membranes thus imparting tolerance to various abiotic stresses.

Plant lipid transfer proteins: are we finally closing in on the roles of these enigmatic proteins?

The nonspecific lipid transfer proteins (LTPs) are small compact proteins folded around a tunnel-like hydrophobic cavity, making them suitable for lipid binding and transport. LTPs are encoded by large gene families in all land plants, but they have not been identified in algae or any other organisms. Thus, LTPs are considered key proteins for plant survival on and colonization of land. LTPs are abundantly expressed in most plant tissues, both above and below ground. They are usually localized to extracellular spaces outside the plasma membrane. Although the in vivo functions of LTPs remain unclear, accumulating evidence suggests a role for LTPs in the transfer and deposition of monomers required for assembly of the waterproof lipid barriers, such as cutin and cuticular wax, suberin, and sporopollenin, formed on many plant surfaces. Some LTPs may be involved in other processes, such as signaling during pathogen attacks. Here, we present the current status of LTP research with a focus on the role of these proteins in lipid barrier deposition and cell expansion. We suggest that LTPs facilitate extracellular transfer of barrier materials and adhesion between barriers and extracellular materials. A growing body of research may uncover the true role of LTPs in plants.

Asymmetric Evolution and Expansion of the NAC Transcription Factor in Polyploidized Cotton

Polyploidy in Gossypium hirsutum conferred different properties from its diploid ancestors under the regulation of transcription factors. The NAC transcription factor is a plant-specific family that can be related to plant growth and development. So far, little is known about the NAC family in cotton. This study identified 495 NAC genes in three cotton species and investigated the evolution and expansion of different genome-derived NAC genes in cotton. We revealed 15 distinct NAC subfamilies in cotton. Different subfamilies had different gene proportions, expansion rate, gene loss rate, and orthologous exchange rate. Paleohexaploidization (35%) and cotton-specific decaploidy (32%) might have primarily led to the expansion of the NAC family in cotton. Half of duplication events in G. hirsutum were inherited from its diploid ancestor, and others might have occurred after interspecific hybridization. In addition, NAC genes in the At and Dt subgenomes displayed asymmetric molecular evolution, as evidenced by their different gene loss rates, orthologous exchange, evolutionary rates, and expression levels. The dominant duplication event was different during the cotton evolutionary history. Different genome-derived NACs might have interacted with each other, which ultimately resulted in morphogenetic evolution. This study delineated the expansion and evolutionary history of the NAC family in cotton and illustrated the different fates of NAC genes during polyploidization.