scholarly journals Genome-Wide Identification and Comparison of Cysteine Proteases in the Pollen Coat and Other Tissues in Maize

2021 ◽  
Vol 12 ◽  
Author(s):  
Yanhua Li ◽  
Liangjie Niu ◽  
Xiaolin Wu ◽  
Claudia Faleri ◽  
Fuju Tai ◽  
...  
Keyword(s):  
Growth And Development ◽  
Cellular Localization ◽  
Expression Patterns ◽  
Sodium Dodecyl ◽  
Cysteine Proteases ◽  
Immunogold Electron Microscopy ◽  
Upstream Sequence ◽  
Maize Pollen ◽  
Genome Wide ◽  
Pollen Coat

Cysteine proteases, belonging to the C1-papain family, play a major role in plant growth and development, senescence, and immunity. There is evidence to suggest that pollen cysteine protease (CP) (ZmCP03) is involved in regulating the anther development and pollen formation in maize. However, there is no report on the genome-wide identification and comparison of CPs in the pollen coat and other tissues in maize. In this study, a total of 38 homologous genes of ZmCP03 in maize were identified. Subsequently, protein motifs, conserved domains, gene structures, and duplication patterns of 39 CPs are analyzed to explore their evolutionary relationship and potential functions. The cis-elements were identified in the upstream sequence of 39 CPs, especially those that are related to regulating growth and development and responding to environmental stresses and hormones. The expression patterns of these genes displayed remarked difference at a tissue or organ level in maize based on the available transcriptome data in the public database. Quantitative reverse transcription PCR (RT-qPCR) analysis showed that ZmCP03 was preferably expressed at a high level in maize pollen. Analyses by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and immunoblot, immunofluorescence and immunogold electron microscopy all validated the cellular localization of ZmCP03 in both the pollen coat and pollen cytoplasm. In addition, 142 CP genes from Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa) and cotton (Gossypium hirsutum), together with 39 maize CPs, were retrieved to analyze their evolution by comparing with orthologous genes. The results suggested that ZmCP03 was relatively conservative and stable during evolution. This study may provide a referential evidence on the function of ZmCP03 in pollen development and germination in maize.

scholarly journals Genome-wide identification and expression analysis of NADPH oxidase genes in response to ABA and abiotic stresses, and in fibre formation in Gossypium

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8404 ◽  
Author(s):  
Gaofeng Zhang ◽  
Caimeng Yue ◽  
Tingting Lu ◽  
Lirong Sun ◽  
Fushun Hao
Keyword(s):  
Abiotic Stresses ◽  
Growth And Development ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Fiber Formation ◽  
Biotic And Abiotic Stresses ◽  
Fibre Formation ◽  
Genome Wide ◽  
Regulation Mechanisms ◽  
Respiratory Burst Oxidase

Plasma membrane NADPH oxidases, also named respiratory burst oxidase homologues (Rbohs), play pivotal roles in many aspects of growth and development, as well as in responses to hormone signalings and various biotic and abiotic stresses. Although Rbohs family members have been identified in several plants, little is known about Rbohs in Gossypium. In this report, we characterized 13, 13, 26 and 19 Rbohs in G. arboretum, G. raimondii, G. hirsutum and G. barbadense, respectively. These Rbohs were conservative in physical properties, structures of genes and motifs. The expansion and evolution of the Rbohs dominantly depended on segmental duplication, and were under the purifying selection. Transcription analyses showed that GhRbohs were expressed in various tissues, and most GhRbohs were highly expressed in flowers. Moreover, different GhRbohs had very diverse expression patterns in response to ABA, high salinity, osmotic stress and heat stress. Some GhRbohs were preferentially and specifically expressed during ovule growth and fiber formation. These results suggest that GhRbohs may serve highly differential roles in mediating ABA signaling, in acclimation to environmental stimuli, and in fiber growth and development. Our findings are valuable for further elucidating the functions and regulation mechanisms of the Rbohs in adaptation to diverse stresses, and in growth and development in Gossypium.

scholarly journals Genome-wide identification, genomic organization, and expression profiling of the CONSTANS-like (COL) gene family in petunia under multiple stresses

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Khadiza Khatun ◽  
Sourav Debnath ◽  
Arif Hasan Khan Robin ◽  
Antt Htet Wai ◽  
Ujjal Kumar Nath ◽  
...  
Keyword(s):  
Stress Response ◽  
Plant Growth ◽  
Growth And Development ◽  
Sequence Similarity ◽  
Expression Patterns ◽  
Plant Growth And Development ◽  
Specific Expression ◽  
Systematic Analysis ◽  
Genome Wide ◽  
A Genome

Abstract Background CONSTANS-like (CO-like, COL) are putative zinc-finger transcription factors known to play vital role in various plant biological processes such as control of flowering time, regulation of plant growth and development and responses to stresses. However, no systematic analysis of COL family gene regarding the plant development and stress response has been previously performed in any solanaceous crop. In the present study, a comprehensive genome-wide analysis of COL family genes in petunia has been conducted to figure out their roles in development of organs and stress response. Results A total of 33 COL genes, 15 PaCOL genes in P. axillaris and 18 PiCOL genes in P. inflata, were identified in petunia. Subsequently, a genome-wide systematic analysis was performed in 15 PaCOL genes. Considering the domain composition and sequence similarity the 15 PaCOL and 18 PiCOL genes were phylogenetically classified into three groups those are conserved among the flowering plants. Moreover, all of the 15 PaCOL proteins were localized in nucleus. Furthermore, differential expression patterns of PaCOL genes were observed at different developmental stages of petunia. Additionally, transcript expression of 15 PaCOL genes under various abiotic and phytohormone treatments showed their response against stresses. Moreover, several cis-elements related to stress, light-responsive, hormone signaling were also detected in different PaCOL genes. Conclusion The phylogenetic clustering, organ specific expression pattern and stress responsive expression profile of conserved petunia COL genes indicating their involvement in plant growth and development and stress response mechanism. This work provide a significant foundation for understanding the biological roles of petunia COL genes in plant growth, development and in stress response.

scholarly journals Genome-wide analysis of BBX gene family in Tartary buckwheat (Fagopyrum tataricum)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11939
Author(s):  
Jiali Zhao ◽  
Hongyou Li ◽  
Juan Huang ◽  
Taoxiong Shi ◽  
Ziye Meng ◽  
...  
Keyword(s):  
Growth And Development ◽  
Environmental Changes ◽  
Anthocyanin Biosynthesis ◽  
Expression Patterns ◽  
Tartary Buckwheat ◽  
Chromosome 6 ◽  
Fagopyrum Tataricum ◽  
Conserved Motifs ◽  
Genome Wide ◽  
Gene Structures

BBX (B-box), a zinc finger transcription factor with one or two B-box domains, plays an important role in plant photomorphogenesis, growth, and development as well as response to environmental changes. In this study, 28 Tartary buckwheat BBX (FtBBX) genes were identified and screened using a comparison program. Their physicochemical properties, gene structures, conserved motifs, distribution in chromosomal, and phylogeny of the coding proteins, as well as their expression patterns, were analyzed. In addition, multiple collinearity analysis in three monocots and three dicot species illustrated that the BBX proteins identified from monocots clustered separately from those of dicots. Moreover, the expression of 11 candidate BBX genes with probable involvement in the regulation of anthocyanin biosynthesis was analyzed in the sprouts of Tartary buckwheat during light treatment. The results of gene structure analysis showed that all the 28 BBX genes contained B-box domain, three genes lacked introns, and these genes were unevenly distributed on the other seven chromosomes except for chromosome 6. The 28 proteins contained 10 conserved motifs and could be divided into five subfamilies. BBX genes of Tartary buckwheat showed varying expression under different conditions demonstrating that FtBBXs might play important roles in Tartary buckwheat growth and development. This study lays a foundation for further understanding of Tartary buckwheat BBX genes and their functions in growth and development as well as regulation of pigmentation in Tartary buckwheat.

scholarly journals Genome-wide survey of soybean papain-like cysteine proteases and their expression analysis in root nodule symbiosis

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Songli Yuan ◽  
Danxia Ke ◽  
Rong Li ◽  
Xiangyong Li ◽  
Lei Wang ◽  
...  
Keyword(s):  
Root Nodule ◽  
Expression Patterns ◽  
Cysteine Proteases ◽  
Nodule Development ◽  
Whole Genome ◽  
Root Nodule Symbiosis ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Survey ◽  
Nodule Symbiosis

Abstract Background Plant papain-like cysteine proteases (PLCPs) are a large class of proteolytic enzymes and play important roles in root nodule symbiosis (RNS), while the whole-genome studies of PLCP family genes in legume are quite limited, and the roles of Glycine max PLCPs (GmPLCPs) in nodulation, nodule development and senescence are not fully understood. Results In the present study, we identified 97 GmPLCPs and performed a genome-wide survey to explore the expansion of soybean PLCP family genes and their relationships to RNS. Nineteen paralogous pairs of genomic segments, consisting of 77 GmPLCPs, formed by whole-genome duplication (WGD) events were identified, showing a high degree of complexity in duplication. Phylogenetic analysis among different species showed that the lineage differentiation of GmPLCPs occurred after family expansion, and large tandem repeat segment were specifically in soybean. The expression patterns of GmPLCPs in symbiosis-related tissues and nodules identified RNS-related GmPLCPs and provided insights into their putative symbiotic functions in soybean. The symbiotic function analyses showed that a RNS-related GmPLCP gene (Glyma.04G190700) really participate in nodulation and nodule development. Conclusions Our findings improved our understanding of the functional diversity of legume PLCP family genes, and provided insights into the putative roles of the legume PLCPs in nodulation, nodule development and senescence.

Cryptostatin, a chagasin-family cysteine protease inhibitor of Cryptosporidium parvum

Parasitology ◽  
2012 ◽  
Vol 139 (8) ◽  
pp. 1029-1037 ◽  
Author(s):  
J.-M. KANG ◽  
H.-L. JU ◽  
J.-R. YU ◽  
W.-M. SOHN ◽  
B.-K. NA
Keyword(s):  
Cryptosporidium Parvum ◽  
Cysteine Protease ◽  
Cathepsin L ◽  
Sodium Dodecyl ◽  
Cysteine Proteases ◽  
Cysteine Protease Inhibitor ◽  
Immunogold Electron Microscopy ◽  
Electron Microscopy Analysis ◽  
Wide Ph Range ◽  
Human Cathepsin

SUMMARYCysteine proteases of pathogenic protozoan parasites play pivotal roles in the life cycle of parasites, but strict regulation of their activities is also essential for maintenance of parasite physiology and interaction with hosts. In this study, we identified and characterized cryptostatin, a novel inhibitor of cysteine protease (ICP) of Cryptosporidium parvum. Cryptostatin showed low sequence identity to other chagasin-family ICPs, but 3 motifs (NPTTG, GXGG, and RPW/F motifs), which are evolutionarily conserved in chagasin-family ICPs, were found in the sequence. The overall structure of cryptostatin consisted of 8 β-strands that progressed in parallel and closely resembled the immunoglobulin fold. Recombinant cryptostatin inhibited various cysteine proteases, including papain, human cathepsin B, human cathepsin L, and cryptopain-1, with Ki's in the picomolar range. Cryptostatin was active over a wide pH range and was highly stable under physiological conditions. The protein was thermostable and retained its inhibitory activity even after incubation at 95°C. Cryptostatin formed tight complexes with cysteine proteases, so the complexes remained intact in the presence of sodium dodecyl sulfate and β-mercaptoethanol, but they were disassembled by boiling. An immunogold electron microscopy analysis demonstrated diffused localization of cryptostatin within oocystes and meronts, but not within trophozoites, which suggests a possible role for cryptostatin in host cell invasion by C. parvum.

scholarly journals Genome-wide identification and transcript analysis of TCP transcription factors in grapevine

2019 ◽  
Author(s):  
xiangpeng leng ◽  
Hongru Wei ◽  
Xiaozhao Xu ◽  
Sandip A. Ghuge ◽  
Dongjie Jia ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Plant Growth ◽  
Fruit Development ◽  
Growth And Development ◽  
Expression Patterns ◽  
Class Ii ◽  
Plant Growth And Development ◽  
Specific Expression ◽  
Genome Wide ◽  
Tcp Family

Abstract Background The plant-specific TCP transcription factors play different functions in multiple processes of plant growth and development. TCP family genes have been identified in several plant species, but no comprehensive analysis of the TCP family in grapevine has been undertaken to date, especially their roles in fruit development. Results A total of 18 non-redundant grapevine TCP (VvTCP) genes distributing on 11 chromosomes were identified. Phylogenetic and structural analysis showed that VvTCP genes were divided into two main classes - class I and class II. The Class II genes were further classified into two subclasses, the CIN subclass and the CYC/TB1 subclass. Segmental duplication was a predominant duplication event which caused the expansion of VvTCP genes. The cis-acting elements analysis and tissue-specific expression patterns of VvTCP genes demonstrated that these VvTCP genes might play important roles in plant growth and development. Expression patterns of VvTCP genes during fruit development and ripening were analyzed by RNA-Seq and qRT-PCR. Among them, eleven VvTCP genes were down-regulated during different fruit developmental stages, while only one VvTCP genes were up-regulated, suggesting that most VvTCP genes were probably related to early development in grapevine fruit. Futhermore, the expression of most VvTCP genes can be inhibited by drought and waterlogging stresses. Conclusions Our study establishes the first genome-wide analysis of the grapevine TCP gene family and provides valuable information for understanding the classification and functions of the TCP genes in grapevine.

scholarly journals An Expression-Driven Approach to the Prediction of Carbohydrate Transport and Utilization Regulons in theHyperthermophilic Bacterium Thermotoga maritima

2005 ◽  
Vol 187 (21) ◽  
pp. 7267-7282 ◽  
Author(s):  
Shannon B. Conners ◽  
Clemente I. Montero ◽  
Donald A. Comfort ◽  
Keith R. Shockley ◽  
Matthew R. Johnson ◽  
...  
Keyword(s):  
Abc Transporters ◽  
Mixed Model ◽  
Thermotoga Maritima ◽  
Expression Patterns ◽  
Pentose Phosphate ◽  
Transport Systems ◽  
Upstream Sequence ◽  
Mixed Model Analysis ◽  
Microarray Expression Data ◽  
Genome Wide

ABSTRACT Comprehensive analysis of genome-wide expression patterns during growth of the hyperthermophilic bacterium Thermotoga maritima on 14 monosaccharide and polysaccharide substrates was undertaken with the goal of proposing carbohydrate specificities for transport systems and putative transcriptional regulators. Saccharide-induced regulons were predicted through the complementary use of comparative genomics, mixed-model analysis of genome-wide microarray expression data, and examination of upstream sequence patterns. The results indicate that T. maritima relies extensively on ABC transporters for carbohydrate uptake, many of which are likely controlled by local regulators responsive to either the transport substrate or a key metabolic degradation product. Roles in uptake of specific carbohydrates were suggested for members of the expanded Opp/Dpp family of ABC transporters. In this family, phylogenetic relationships among transport systems revealed patterns of possible duplication and divergence as a strategy for the evolution of new uptake capabilities. The presence of GC-rich hairpin sequences between substrate-binding proteins and other components of Opp/Dpp family transporters offers a possible explanation for differential regulation of transporter subunit genes. Numerous improvements to T. maritima genome annotations were proposed, including the identification of ABC transport systems originally annotated as oligopeptide transporters as candidate transporters for rhamnose, xylose, β-xylan, andβ -glucans and identification of genes likely to encode proteins missing from current annotations of the pentose phosphate pathway. Beyond the information obtained for T. maritima, the present study illustrates how expression-based strategies can be used for improving genome annotation in other microorganisms, especially those for which genetic systems are unavailable.

scholarly journals Genome-wide analysis of structures and characteristics of the SPL gene family in wheat (Triticum aestivum L.)

2020 ◽  
Author(s):  
Li Li ◽  
Fu Shi ◽  
Yanbin Guan ◽  
Guoli Wang ◽  
Yufan Zhang ◽  
...  
Keyword(s):  
Gene Family ◽  
Growth And Development ◽  
Expression Patterns ◽  
Transcript Level ◽  
Triticum Aestivum L ◽  
Wheat Genome ◽  
Systematic Analysis ◽  
Genome Wide ◽  
Flowering Regulation ◽  
Hormone Signals

Abstract Background: The SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) genes encode a family of plant-specific transcription factors that contain a conservative SBP domain. SPL proteins play important roles in plant growth and development, such as plant architecture, flowering regulation, and grain yield. However, the systematic analysis of TaSPL gene family in wheat is lacking.Results: In this study, 56 TaSPL genes were identified from wheat genome and divided into eight groups (G1-G8), according to the phylogenetic analysis of TaSPL proteins among numbers of plant species. Bioinformatics method were applied to analyse the gene structure, motif, chromosome localization, segmental duplication and synteny of total TaSPL genes and the results showed that their characteristics were different among group in the exon-intron constitution, conserved and specific motif. The expansion and evolution of the TaSPL genes occurred within the wheat genome. Total 28 of 56 TaSPL genes were predicted to be putative targets for miR156, which revealed the importance of miR156-mediated regulation in wheat. Moreover, transcript level analysis of TaSPL genes in wheat tissues by qRT-PCR discovered the diversified spatiotemporal expression patterns, based on the comparison with reference RNA-seq data. Some TaSPL genes were subject to various stress treatments including drought and hormones, etc. suggesting that these part genes probably involved in responding to hormone signals during different wheat development stages. Conclusions: Our findings show that TaSPL genes may regulate the development of spike and grain, resistance to abiotic stresses, and involve in responding to hormone signals. These results could provide a fundamentally information to further study of the functions of TaSPL genes in wheat growth and development.

Genome-wide identification and expression analysis of the SPL gene family in woodland strawberry Fragaria vesca

Genome ◽  
2018 ◽  
Vol 61 (9) ◽  
pp. 675-683 ◽  
Author(s):  
Jin-Song Xiong ◽  
Dan Zheng ◽  
Hong-Yu Zhu ◽  
Jian-Qiu Chen ◽  
Ran Na ◽  
...  
Keyword(s):  
Expression Analysis ◽  
Growth And Development ◽  
Expression Patterns ◽  
Systematic Research ◽  
Fragaria Vesca ◽  
Woodland Strawberry ◽  
Genome Wide ◽  
Squamosa Promoter Binding Protein ◽  
Spl Genes ◽  
Localization Analysis

SQUAMOSA promoter-binding protein-like (SPL) is a class of plant-specific transcription factors that play critical roles in regulating plant growth and development. However, little systematic research on SPL genes has been conducted in strawberry. In this study, 14 SPL genes were identified in the genome of woodland strawberry (Fragaria vesca), one of the model plants of the family Rosaceae. Chromosome localization analysis indicated that the 14 FvSPL genes were unevenly distributed on six chromosomes. Phylogenetic analysis indicated that the FvSPL proteins could be clustered into six groups (G1 to G6). Genes with similar structure were classified into the same group, implying their functional redundancy. In addition, nine out of the 14 FvSPL genes, belonging to G1, G2, and G5, were found to be the putative targets of FvmiR156 genes. Expression analysis indicated FvSPL genes exhibited highly diverse expression patterns in the tissues and organs examined. The transcript levels of most FvmiR156-targeted FvSPL genes in fruit were lower than those non-miR156-targeted genes. In addition, the expression of the FvmiR156-targeted FvSPL genes decreased during fruit ripening, whereas the expression of FvmiR156 genes increased in fruit during this process. The results provide a foundation for future functional analysis of FvSPL genes in strawberry growth and development.

scholarly journals Genome-Wide Identification and Expression Analysis of the MADS-Box Gene Family in Sweet Potato [Ipomoea batatas (L.) Lam]

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhengwei Shao ◽  
Minhong He ◽  
Zhipeng Zeng ◽  
Yanzhu Chen ◽  
Amoanimaa-Dede Hanna ◽  
...  
Keyword(s):  
Sweet Potato ◽  
Growth And Development ◽  
Ipomoea Batatas ◽  
Expression Patterns ◽  
Tuberous Root ◽  
Mads Box ◽  
Mads Box Genes ◽  
Fibrous Root ◽  
Genome Wide ◽  
Mads Box Gene

MADS-box gene, one of the largest transcription factor families in plants, is a class of transcription factors widely present in eukaryotes. It plays an important role in plant growth and development and participates in the growth and development of flowers and fruits. Sweet potato is the seventh most important food crop in the world. Its tuberous roots, stems, and leaves contain a large number of proteins, lipids, carotenoids, anthocyanins, conjugated phenolic acids, and minerals, which have high edible, forage, and medicinal value, and is also an important energy crop. At present, MADS-box genes in sweet potato have rarely been reported, and there has been no study on the genome-wide identification and classification of MADS-box genes in Ipomoea batatas. This study provided the first comprehensive analysis of sweet potato MADS-box genes. We identified 95 MADS-box genes, analyzed the structure and protein of sweet potato MADS-box genes, and categorized them based on phylogenetic analysis with Arabidopsis MADS-box proteins. Chromosomal localization indicated an unequal number of MADS-box genes in all 14 chromosomes except LG3, with more than 10 MADS-box genes located on chromosomes LG7, LG11, and LG15. The MADS domain and core motifs of the sweet potato MADS-box genes were identified by motif analysis. We identified 19 MADS-box genes with collinear relationships and analyzed duplication events. Cis-acting elements, such as light-responsive, auxin-responsive, drought-inducible, and MeJA-responsive elements, were found in the promoter region of the MADS-box genes in sweet potato, which further indicates the basis of MADS-box gene regulation in response to environmental changes and hormones. RNA-seq suggested that sweet potato MADS-box genes exhibit tissue-specific expression patterns, with 34 genes highly expressed in sweet potato flowers and fruits, and 19 genes highly expressed in the tuberous root, pencil root, or fibrous root. qRT-PCR again validated the expression levels of the 10 genes and found that IbMADS1, IbMADS18, IbMADS19, IbMADS79, and IbMADS90 were highly expressed in the tuberous root or fibrous root, and IbMADS18, IbMADS31, and IbMADS83 were highly expressed in the fruit. In this study, the molecular basis of MADS-box genes of sweet potato was analyzed from various angles. The effects of MADS-box genes on the growth and development of sweet potato were investigated, which may provide a certain theoretical basis for molecular breeding of sweet potato.

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