Branchial expression patterns of claudin isoforms in Atlantic salmon during seawater acclimation and smoltification

In euryhaline teleosts, permeability changes in gill epithelia are essential during acclimation to changed salinity. This study examined expression patterns of branchial tight junction proteins called claudins, which are important determinants of ion selectivity and general permeability in epithelia. We identified Atlantic salmon genes belonging to the claudin family by screening expressed sequence tag libraries available at NCBI, and classification was performed with the aid of maximum likelihood analysis. In gill libraries, five isoforms (10e, 27a, 28a, 28b, and 30) were present, and quantitative PCR analysis confirmed tissue-specific expression in gill when compared with kidney, intestine, heart, muscle, brain, and liver. Expression patterns during acclimation of freshwater salmon to seawater (SW) and during the smoltification process were examined. Acclimation to SW reduced the expression of claudin 27a and claudin 30 but had no overall effect on claudin 28a and claudin 28b. In contrast, SW induced a fourfold increase in expression of claudin 10e. In accord, a peak in branchial claudin 10e was observed during smoltification in May, coinciding with optimal SW tolerance. Smoltification induced no significant changes in expression of the other isoforms. This study demonstrates the expression of an array of salmon claudin isoforms and shows that SW acclimation involves inverse regulation, in the gill, of claudin 10e vs. claudin 27a and 30. It is possible that claudin 10e is an important component of cation selective channels, whereas reduction in claudin 27a and 30 may change permeability conditions in favor of the ion secretory mode of the SW gill.

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Transcription Profiles of Age-at-Maturity-Associated Genes Suggest Cell Fate Commitment Regulation as a Key Factor in the Atlantic Salmon Maturation Process

G3 Genes|Genome|Genetics ◽

10.1534/g3.119.400882 ◽

2019 ◽

Vol 10 (1) ◽

pp. 235-246 ◽

Cited By ~ 3

Author(s):

Johanna Kurko ◽

Paul V. Debes ◽

Andrew H. House ◽

Tutku Aykanat ◽

Jaakko Erkinaro ◽

...

Keyword(s):

Atlantic Salmon ◽

Cell Fate ◽

Molecular Mechanisms ◽

Genome Wide Association Study ◽

Expression Patterns ◽

Hippo Signaling ◽

Age At Maturity ◽

Specific Expression ◽

Hpg Axis ◽

Tissue Specific

Despite recent taxonomic diversification in studies linking genotype with phenotype, follow-up studies aimed at understanding the molecular processes of such genotype-phenotype associations remain rare. The age at which an individual reaches sexual maturity is an important fitness trait in many wild species. However, the molecular mechanisms regulating maturation timing processes remain obscure. A recent genome-wide association study in Atlantic salmon (Salmo salar) identified large-effect age-at-maturity-associated chromosomal regions including genes vgll3, akap11 and six6, which have roles in adipogenesis, spermatogenesis and the hypothalamic-pituitary-gonadal (HPG) axis, respectively. Here, we determine expression patterns of these genes during salmon development and their potential molecular partners and pathways. Using Nanostring transcription profiling technology, we show development- and tissue-specific mRNA expression patterns for vgll3, akap11 and six6. Correlated expression levels of vgll3 and akap11, which have adjacent chromosomal location, suggests they may have shared regulation. Further, vgll3 correlating with arhgap6 and yap1, and akap11 with lats1 and yap1 suggests that Vgll3 and Akap11 take part in actin cytoskeleton regulation. Tissue-specific expression results indicate that vgll3 and akap11 paralogs have sex-dependent expression patterns in gonads. Moreover, six6 correlating with slc38a6 and rtn1, and Hippo signaling genes suggests that Six6 could have a broader role in the HPG neuroendrocrine and cell fate commitment regulation, respectively. We conclude that Vgll3, Akap11 and Six6 may influence Atlantic salmon maturation timing via affecting adipogenesis and gametogenesis by regulating cell fate commitment and the HPG axis. These results may help to unravel general molecular mechanisms behind maturation.

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Insights into the Superoxide Dismutase Gene Family and Its Roles in Dendrobium catenatum under Abiotic Stresses

Plants ◽

10.3390/plants9111452 ◽

2020 ◽

Vol 9 (11) ◽

pp. 1452

Author(s):

Hui Huang ◽

Hui Wang ◽

Yan Tong ◽

Yuhua Wang

Keyword(s):

Superoxide Dismutase ◽

Gene Family ◽

Abiotic Stresses ◽

Phylogenetic Analyses ◽

Expression Patterns ◽

Light Response ◽

Vital Role ◽

Pcr Analysis ◽

Specific Expression ◽

Expression Levels

Dendrobium catenatum is a member of epiphytic orchids with extensive range of pharmacological properties and ornamental values. Superoxide dismutase (SOD), a key member of antioxidant system, plays a vital role in protecting plants against oxidative damage caused by various biotic and abiotic stresses. So far, little is known about the SOD gene family in D. catenatum. In this study, eight SOD genes, including four Cu/ZnSODs, three FeSODs and one MnSOD, were identified in D. catenatum genome. Phylogenetic analyses of SOD proteins in D. catenatum and several other species revealed that these SOD proteins can be assigned to three subfamilies based on their metal co-factors. Moreover, the similarities in conserved motifs and gene structures in the same subfamily corroborated their classification and inferred evolutionary relationships. There were many hormone and stress response elements in DcaSODs, of which light responsiveness elements was the largest group. All DcaSODs displayed tissue-specific expression patterns and exhibited abundant expression levels in flower and leaf. According to public RNA-seq data and qRT-PCR analysis showed that the almost DcaSODs, except for DcaFSD2, were highly expressed under cold and drought treatments. Under heat, light, and salt stresses, DcaCSD1, DcaCSD2, DcaCSD3 were always significantly up-regulated, which may play a vital role in coping with various stresses. The expression levels of DcaFSD1 and DcaFSD2 were promoted by high light, suggesting their important roles in light response. These findings provided valuable information for further research on DcaSODs in D. catenatum.

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Genome-wide identification and expression profiling of the C2H2-type zinc finger protein genes in the silkworm Bombyx mori

PeerJ ◽

10.7717/peerj.7222 ◽

2019 ◽

Vol 7 ◽

pp. e7222

Author(s):

SongYuan Wu ◽

Xiaoling Tong ◽

ChunLin Li ◽

KunPeng Lu ◽

Duan Tan ◽

...

Keyword(s):

Zinc Finger ◽

Binding Sites ◽

Zinc Finger Protein ◽

Gene Annotation ◽

Expression Patterns ◽

Fruit Fly ◽

Expression Level ◽

Pcr Analysis ◽

Female Reproduction ◽

Specific Expression

Cys2-His2 zinc finger (C2H2-ZF) proteins comprise the largest class of putative eukaryotic transcription factors. The zinc finger motif array is highly divergent, indicating that most proteins will have distinctive binding sites and perform different functions. However, the binding sites and functions of the majority of C2H2-ZF proteins remain unknown. In this study, we identified 327 C2H2-ZF protein genes in the silkworm, 290 in the monarch butterfly, 243 in the fruit fly, 107 in elegans, 673 in mouse, and 1,082 in human. The C2H2-ZF protein genes of the silkworm were classified into three main grouping clades according to a phylogenetic classification, and 312 of these genes could be mapped onto 27 chromosomes. Most silkworm C2H2-ZF protein genes exhibited specific expression in larval tissues. Furthermore, several C2H2-ZF protein genes had sex-specific expression during metamorphosis. In addition, we found that some C2H2-ZF protein genes are involved in metamorphosis and female reproduction by using expression clustering and gene annotation analysis. Among them, five genes were selected, BGIBMGA002091 (CTCF), BGIBMGA006492 (fru), BGIBMGA006230 (wor), BGIBMGA004640 (lola), and BIGBMGA004569, for quantitative real-time PCR analysis from larvae to adult ovaries. The results showed that the five genes had different expression patterns in ovaries, among which BGIBMGA002091 (CTCF) gene expression level was the highest, and its expression level increased rapidly in late pupae and adult stages. These findings provide a basis for further investigation of the functions of C2H2-ZF protein genes in the silkworm, and the results offer clues for further research into the development of metamorphosis and female reproduction in the silkworm.

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Genome-wide identification of growth-regulating factors in moso bamboo (Phyllostachys edulis): in silico and experimental analyses

PeerJ ◽

10.7717/peerj.7510 ◽

2019 ◽

Vol 7 ◽

pp. e7510 ◽

Cited By ~ 4

Author(s):

Yanan Shi ◽

Huanlong Liu ◽

Yameng Gao ◽

Yujiao Wang ◽

Min Wu ◽

...

Keyword(s):

Expression Patterns ◽

Purifying Selection ◽

Synonymous Substitution ◽

Moso Bamboo ◽

Bimolecular Fluorescence Complementation ◽

Pcr Analysis ◽

Hormone Regulation ◽

In Planta ◽

Phyllostachys Edulis ◽

Specific Expression

Growth-regulating factor (GRF), a small plant-specific transcription factor (TF) family, is extensively involved in the regulation of growth and developmental processes. However, the GRF family has not been comprehensively studied in moso bamboo (Phyllostachys edulis), a typical non-timber forest member. Here, 18 GRF genes were identified and characterized from the moso bamboo genome, and they clustered into three subfamilies (A, B and C). PeGRF genes were analyzed to determine their gene structures, conserved motifs and promoter. The non-synonymous/synonymous substitution ratios of paralogous and orthologous were less than 1, indicating that the GRF family mainly experienced purifying selection during evolution. According to the analysis of tissue-specific expression patterns, the participation of moso bamboo GRFs might be required during the formation and development of these five tissues. Moreover, PeGRF proteins might be involved in the regulation of plant development in biological processes. The qRT-PCR analysis demonstrated that PeGRF genes played essential roles in combating hormonal stresses and they might be involved in hormone regulation. PeGRF11, a nuclear localized protein as assessed by a subcellular localization assay, could interact with PeGIF3 in yeast and in planta according to yeast two-hybridization and bimolecular fluorescence complementation assays (BiFC) assays. But PeGRF11, as a TF, had no transcriptional activity in yeast. These results provide useful information for future functional research on the GRF genes in moso bamboo.

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Genome-wide identification and expression analysis of ADP-ribosylation factors associated with biotic and abiotic stress in wheat (Triticum aestivum L.)

PeerJ ◽

10.7717/peerj.10963 ◽

2021 ◽

Vol 9 ◽

pp. e10963 ◽

Cited By ~ 1

Author(s):

Yaqian Li ◽

Jinghan Song ◽

Guang Zhu ◽

Zehao Hou ◽

Lin Wang ◽

...

Keyword(s):

Triticum Aestivum ◽

Abiotic Stress ◽

Intracellular Transport ◽

Expression Patterns ◽

Functional Characterization ◽

Triticum Aestivum L ◽

Pcr Analysis ◽

Biotic And Abiotic Stress ◽

Specific Expression ◽

Wheat Varieties

The ARF gene family plays important roles in intracellular transport in eukaryotes and is involved in conferring tolerance to biotic and abiotic stresses in plants. To explore the role of these genes in the development of wheat (Triticum aestivum L.), 74 wheat ARF genes (TaARFs; including 18 alternate transcripts) were identified and clustered into seven sub-groups. Phylogenetic analysis revealed that TaARFA1 sub-group genes were strongly conserved. Numerous cis-elements functionally associated with the stress response and hormones were identified in the TaARFA1 sub-group, implying that these TaARFs are induced in response to abiotic and biotic stresses in wheat. According to available transcriptome data and qRT-PCR analysis, the TaARFA1 genes displayed tissue-specific expression patterns and were regulated by biotic stress (powdery mildew and stripe rust) and abiotic stress (cold, heat, ABA, drought and NaCl). Protein interaction network analysis further indicated that TaARFA1 proteins may interact with protein phosphatase 2C (PP2C), which is a key protein in the ABA signaling pathway. This comprehensive analysis will be useful for further functional characterization of TaARF genes and the development of high-quality wheat varieties.

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Identification, structure, and differential expression of members of a BURP domain containing protein family in soybean

Genome ◽

10.1139/g02-032 ◽

2002 ◽

Vol 45 (4) ◽

pp. 693-701 ◽

Cited By ~ 30

Author(s):

Cheryl Granger ◽

Virginia Coryell ◽

Anupama Khanna ◽

Paul Keim ◽

Lila Vodkin ◽

...

Keyword(s):

Glycine Max ◽

Gene Duplication ◽

Expressed Sequence Tag ◽

Signal Sequence ◽

Expression Patterns ◽

Family Members ◽

Specific Expression ◽

Burp Domain ◽

Duplication Events ◽

Expressed Sequence

Expressed sequence tags (ESTs) exhibiting homology to a BURP domain containing gene family were identified from the Glycine max (L.) Merr. EST database. These ESTs were assembled into 16 contigs of variable sizes and lengths. Consistent with the structure of known BURP domain containing proteins, the translation products exhibit a modular structure consisting of a C-terminal BURP domain, an N-terminal signal sequence, and a variable internal region. The soybean family members exhibit 3598% similarity in a ~100-amino-acid C-terminal region, and a phylogenetic tree constructed using this region shows that some soybean family members group together in closely related pairs, triplets, and quartets, whereas others remain as singletons. The structure of these groups suggests that multiple gene duplication events occurred during the evolutionary history of this family. The depth and diversity of G. max EST libraries allowed tissue-specific expression patterns of the putative soybean BURPs to be examined. Consistent with known BURP proteins, the newly identified soybean BURPs have diverse expression patterns. Furthermore, putative paralogs can have both spatially and quantitatively distinct expression patterns. We discuss the functional and evolutionary implications of these findings, as well as the utility of EST-based analyses for identifying and characterizing gene families.Key words: BURP domain, expressed sequence tag, gene duplication, Glycine max.

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Allele-specific expression patterns of interleukin-2 and Pax-5 revealed by a sensitive single-cell RT-PCR analysis

Current Biology ◽

10.1016/s0960-9822(00)00565-0 ◽

2000 ◽

Vol 10 (13) ◽

pp. 789-792 ◽

Cited By ~ 52

Author(s):

Kristina L. Rhoades ◽

Nandita Singh ◽

Itamar Simon ◽

Barbara Glidden ◽

Howard Cedar ◽

...

Keyword(s):

Single Cell ◽

Expression Patterns ◽

Interleukin 2 ◽

Pcr Analysis ◽

Rt Pcr ◽

Specific Expression ◽

Allele Specific Expression ◽

Allele Specific

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Functional characterization and expression patterns of PnATX genes under different abiotic stress treatments in Populus

Tree Physiology ◽

10.1093/treephys/tpaa008 ◽

2020 ◽

Vol 40 (4) ◽

pp. 520-537

Author(s):

Zhiru Xu ◽

Jiahuan Huang ◽

Chunpu Qu ◽

Ruhui Chang ◽

Jinyuan Chen ◽

...

Keyword(s):

Salicylic Acid ◽

Metal Binding ◽

Molecular Mechanisms ◽

Expression Patterns ◽

Functional Characterization ◽

Pcr Analysis ◽

Binding Motif ◽

Copper Chaperone ◽

Specific Expression ◽

Relative Expression Level

Abstract The copper chaperone ATX1 has been investigated previously in the herbaceous plants Arabidopsis and rice. However, the molecular mechanisms of ATX1 underlying copper transport and functional characteristics in the woody plant Populus are poorly understood. In this study, PnATX1 and PnATX2 of Populus simonii × P. nigra were identified and characterized. Sequence analysis showed that PnATXs contained the metal-binding motif MXCXXC in the N-terminus and a lysine-rich region. Phylogenetic analysis of ATX protein sequences revealed that PnATXs were clustered in the same group as AtATX1. PnATX proteins were localized in the cytoplasm and nucleus. Tissue-specific expression analysis showed that PnATX1 and PnATX2 were expressed in all analyzed tissues and, in particular, expressed to a higher relative expression level in young leaves. Quantitative real-time PCR analysis indicated that each PnATX gene was differentially expressed in different tissues under treatments with copper, zinc, iron, jasmonate and salicylic acid (SA). The copper-response element GTAC, methyl jasmonate and salicylic acid responsiveness elements and other cis-acting elements were identified in the PnATX1 and PnATX2 promoters. Expression of β-glucuronidase driven by the PnATX1 promoter was observed in the apical meristem of 7-day-old Arabidopsis transgenic seedlings, and the signal strength was not influenced by deficient or excessive copper conditions. Both PnATX1 and PnATX2 functionally rescued the defective phenotypes of yeast atx1Δ and sod1Δ strains. Under copper excess and deficiency conditions, transgenic Arabidopsis atx1 mutants harboring 35S::PnATX constructs exhibited root length and fresh weight similar to those of the wild type and higher than those of Arabidopsis atx1 mutants. Superoxide dismutase activity decreased in transgenic lines compared with that of atx1 mutants, whereas peroxidase and catalase activities increased significantly under excess copper. The results provide a basis for elucidating the role of Populus PnATX genes in copper homeostasis.

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Transcription profiles of age-at-maturity-associated genes suggest cell fate commitment regulation as a key factor in the Atlantic salmon maturation process

10.1101/778498 ◽

2019 ◽

Author(s):

Johanna Kurko ◽

Paul V. Debes ◽

Andrew House ◽

Tutku Aykanat ◽

Jaakko Erkinaro ◽

...

Keyword(s):

Atlantic Salmon ◽

Cell Fate ◽

Molecular Mechanisms ◽

Genome Wide Association Study ◽

Expression Patterns ◽

Hippo Signaling ◽

Age At Maturity ◽

Specific Expression ◽

Hpg Axis ◽

Tissue Specific

AbstractDespite recent taxonomic diversification in studies linking genotype with phenotype, follow-up studies aimed at understanding the molecular processes of such genotype-phenotype associations remain rare. The age at which an individual reaches sexual maturity is an important fitness trait in many wild species. However, the molecular mechanisms regulating maturation timing processes remain obscure. A recent genome-wide association study in Atlantic salmon (Salmo salar) identified large-effect age-at-maturity-associated chromosomal regions including genes vgll3, akap11 and six6, which have roles in adipogenesis, spermatogenesis and the hypothalamic-pituitary-gonadal (HPG) axis, respectively. Here, we determine expression patterns of these genes during salmon development and their potential molecular partners and pathways. Using Nanostring transcription profiling technology, we show development- and tissue-specific mRNA expression patterns for vgll3, akap11 and six6. Correlated expression levels of vgll3 and akap11, which have adjacent chromosomal location, suggests they may have shared regulation. Further, vgll3 correlating with arhgap6 and yap1, and akap11 with lats1 and yap1 suggests that Vgll3 and Akap11 take part in actin cytoskeleton regulation. Tissue-specific expression results indicate that vgll3 and akap11 paralogs have sex-dependent expression patterns in gonads. Moreover, six6 correlating with slc38a6 and rtn1, and Hippo signaling genes suggests that Six6 could have a broader role in the HPG neuroendrocrine and cell fate commitment regulation, respectively. We conclude that Vgll3, Akap11 and Six6 may influence Atlantic salmon maturation timing via affecting on adipogenesis and gametogenesis by regulating cell fate commitment and the HPG axis. These results may help to unravel general molecular mechanisms behind maturation.

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Genomic and Transcriptomic Analysis Reveals Cuticular Protein Genes Responding to Different Insecticides in Fall Armyworm Spodoptera frugiperda

Insects ◽

10.3390/insects12110997 ◽

2021 ◽

Vol 12 (11) ◽

pp. 997

Author(s):

Jia-Ying Zhu ◽

Lu Li ◽

Kai-Ran Xiao ◽

Shu-Qi He ◽

Fu-Rong Gui

Keyword(s):

Spodoptera Frugiperda ◽

Molecular Mechanisms ◽

Developmental Stages ◽

Expression Profiles ◽

Expression Patterns ◽

Fall Armyworm ◽

Pcr Analysis ◽

Rna Seq ◽

Specific Expression ◽

Functional Investigation

The fall armyworm (FAW), Spodoptera frugiperda, is a serious pest of crucial crops causing great threats to the food security of the world. It has evolved resistance to various insecticides, while the underlying molecular mechanisms remain largely unknown. Cuticular proteins (CPs), as primary components in cuticle, play an important role in insects’ protection against environmental stresses. Few of them have been documented as participating in insecticide resistance in several insect species. In order to explore whether CP genes of the FAW exhibit a functional role in responding to insecticides stress, a total of 206 CPs, classified into eight families, were identified from the genome of the FAW through a homology-based approach coupled with manual efforts. The temporal expression profiles of all identified CP genes across developmental stages and their responses to 23 different insecticides were analyzed using the RNA-seq data. Expression profiling indicated that most of the CP genes displayed stage-specific expression patterns. It was found that the expression of 51 CP genes significantly changed after 48 h exposure to 17 different insecticides. The expression of eight CP genes responding to four insecticides were confirmed by RT-PCR analysis. The results showed that their overall expression profiles were consistent with RNA-seq analysis. The findings provide a basis for further functional investigation of CPs implied in insecticide stress in FAW.

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