scholarly journals Genome-wide identification and expression profiling of the PIN auxin transporter gene family in L. chinense

2020 ◽  
Author(s):  
Lingfeng Hu ◽  
Pengkai Wang ◽  
Xiaofei Long ◽  
Weihuang Wu ◽  
Jiaji Zhang ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Structural Characteristics ◽  
Evolutionary Status ◽  
Asymmetric Distribution ◽  
Evolutionary Analysis ◽  
Differential Distribution ◽  
Relict Species ◽  
Specific Expression ◽  
Functional Sites ◽  
Organ Morphogenesis

Abstract BackgroundThe genus Liriodendron is ancient and contains only two species, L. chinense and L. tulipifera. These two Liriodendron sister species, with a typical intercontinental discontinuous distribution in east Asia (L. chinense) and eastern North America (L. tulipifera), have great scientific value for paleobotany systematics. L. chinense is now recognized as an endangered species partially due to its low natural settling rate. In order to improve our understanding of how this species develops and grows and contribute to protecting this valuable relict species from extinction, it is necessary to explore the mechanisms underlying organ morphogenesis and embryonic development, in which auxin plays an important role. The auxin efflux carrier PIN-FORMED (PIN) proteins are required for the polar transport of auxin between cells through their asymmetric distribution on the plasma membrane, thus mediating the differential distribution of auxin in plants and, finally, affecting plant growth and developmental processes.ResultsIn this study, 11 PIN genes were identified in the L. chinense genome. The structural characteristics and evolutionary status of LcPIN genes were thoroughly investigated and interpreted combining physicochemical property analysis, evolutionary analysis, gene structure analysis, chromosomal localization, etc. In addition, motif sequences were used to predict possible functional sites. Further qRT-PCR experiments and transcriptome data analysis indicated that LcPIN genes may potentially play an important role during organ development and somatic embryogenesis in Liriodendron. For example, specific expression of LcPIN3 and LcPIN6a at different developmental stages of stamens and petals suggests their involvement in the development of these organs.ConclusionThis study provides a foundation for further genetic and functional analyses of PIN-mediated auxin patterning during organ morphogenesis and embryogenesis in L. chinense.

scholarly journals Genome-Wide Analysis of the Thioredoxin Gene Family in Gossypium hirsutum L. and the Role of the Atypical Thioredoxin Gene GhTRXL3-2 in Flowering

2021 ◽  
Author(s):  
Hui Liu ◽  
Yunfei Li ◽  
Xianzhong Huang
Keyword(s):  
Gossypium Hirsutum ◽  
Gene Family ◽  
Growth And Development ◽  
Structural Characteristics ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Whole Genome Sequence ◽  
Evolutionary Analysis ◽  
Specific Expression ◽  
Flowering Regulation

AbstractThioredoxin (TRX) is a highly conserved low-molecular-weight protein and a ubiquitous antioxidant enzyme that plays key role in the regulation of plant growth and development. Here, using the whole-genome sequence, we performed a systematic analysis for the TRX gene family in upland cotton (Gossypium hirsutum L.) and analyzed their structural characteristics, evolution, and expression profiles during growth and development. At least 86 GhTRX members, 40 typical and 46 atypical, were identified in the cotton genome, and they were unevenly distributed on the 26 chromosomes. Conserved domains and phylogenic tree construction classified the typical TRX gene family into seven subfamilies and the atypical TRX into nine subfamilies. An evolutionary analysis revealed that the TRX gene family underwent purification selection during evolution. In addition, an RNA-Seq analysis showed that, during vegetative and reproductive development, the differences in transcript abundance levels and organ-specific expression patterns suggest functional diversity. Biochemical assays demonstrated that the atypical TRX protein GhTRXL3-2 interacted with the cotton FLOWERING LOCUS T protein GhFT. The overexpression of GhTRXL3-2 in Arabidopsis thaliana resulted in early flowering compared with control plants. Additionally, the silencing of GhTRXL3-2 in cotton delayed maturation, suggesting that it has important roles in cotton’s flowering regulation. These results help clarify the evolution of the TRX genes and elucidate their biological functions in cotton flowering regulation.

scholarly journals Auxin methylation is required for differential growth inArabidopsis

2018 ◽  
Vol 115 (26) ◽  
pp. 6864-6869 ◽  
Author(s):  
Mohamad Abbas ◽  
Jorge Hernández-García ◽  
Stephan Pollmann ◽  
Sophia L. Samodelov ◽  
Martina Kolb ◽  
...  
Keyword(s):  
Gene Expression ◽  
Auxin Transport ◽  
Polar Auxin Transport ◽  
Asymmetric Distribution ◽  
Loss Of Function ◽  
Differential Growth ◽  
Specific Expression ◽  
Auxin Homeostasis ◽  
Auxin Distribution ◽  
Gene Expression Levels

Asymmetric auxin distribution is instrumental for the differential growth that causes organ bending on tropic stimuli and curvatures during plant development. Local differences in auxin concentrations are achieved mainly by polarized cellular distribution of PIN auxin transporters, but whether other mechanisms involving auxin homeostasis are also relevant for the formation of auxin gradients is not clear. Here we show that auxin methylation is required for asymmetric auxin distribution across the hypocotyl, particularly during its response to gravity. We found that loss-of-function mutants inArabidopsis IAA CARBOXYL METHYLTRANSFERASE1(IAMT1) prematurely unfold the apical hook, and that their hypocotyls are impaired in gravitropic reorientation. This defect is linked to an auxin-dependent increase inPINgene expression, leading to an increased polar auxin transport and lack of asymmetric distribution of PIN3 in theiamt1mutant. Gravitropic reorientation in theiamt1mutant could be restored with either endodermis-specific expression ofIAMT1or partial inhibition of polar auxin transport, which also results in normalPINgene expression levels. We propose that IAA methylation is necessary in gravity-sensing cells to restrict polar auxin transport within the range of auxin levels that allow for differential responses.

The developmental switch in embryonic rho-globin expression is correlated with erythroid lineage-specific differences in transcription factor levels

Development ◽  
1992 ◽  
Vol 115 (4) ◽  
pp. 1149-1164 ◽  
Author(s):  
M.E. Minie ◽  
T. Kimura ◽  
G. Felsenfeld
Keyword(s):  
Transcription Factor ◽  
Developmental Stages ◽  
Globin Gene ◽  
Strongly Correlated ◽  
Binding Studies ◽  
Specific Expression ◽  
Dna Binding Studies ◽  
Translational Start ◽  
Erythroid Development ◽  
Early Developmental

During chicken embryogenesis, the rho-globin gene is expressed only in the early developmental stages. We have examined the mechanisms that are responsible for this behavior. The transcription of the rho-globin gene is strongly correlated with the presence during development of primitive erythroid lineage cells, consistent with the idea that the expression of the rho-globin gene is restricted to that lineage. The “switching off” of rho-globin during development thus reflects the change from primitive to definitive cell lineages which occurs during erythropoiesis in chicken. We use transient expression assays in primary erythroid and other cells to show that the information for lineage- and tissue-specific expression of the rho-globin gene is contained in a 456 bp region upstream of the gene's translational start site. DNA-binding studies, coupled with analysis of the effect on expression of deletions and binding site mutations, were used to identify important control elements within this 456 bp region. We find that binding sites for the ubiquitous transcription factor Sp1, and the specific hematopoietic factor GATA-1, are crucial for expression of the gene in primitive erythroid cells. Quantitative analysis shows that nuclei of the primitive erythroid lineage contain 10-fold more of these factors than do the nuclei of definitive cells. We show that in principle these differences in factor concentration are sufficient to explain the lineage-specific behavior that we observe in our assays. We suggest that this may be an important part of the mechanism for lineage-restricted rho-globin expression during chicken erythroid development. Similar mechanisms may be involved in regulation of other (but not all) members of the globin family.

Spatial- and temporal-restricted pattern for amelogenin gene expression during mouse molar tooth organogenesis

Development ◽  
1988 ◽  
Vol 104 (1) ◽  
pp. 77-85 ◽  
Author(s):  
M.L. Snead ◽  
W. Luo ◽  
E.C. Lau ◽  
H.C. Slavkin
Keyword(s):  
Gene Expression ◽  
In Situ Hybridization ◽  
Gene Transcription ◽  
Developmental Stages ◽  
Three Dimensional ◽  
Molar Tooth ◽  
Specific Expression ◽  
Amelogenin Gene ◽  
Stage Of Development

Position- and time-restricted amelogenin gene transcription was analysed in developing tooth organs using in situ hybridization with asymmetric complementary RNA probes produced from a cDNA specific to the mouse 26 × 10(3) Mr amelogenin. In situ analysis was performed on developmentally staged fetal and neonatal mouse mandibular first (M1) and maxillary first (M1) molar tooth organs using serial sections and three-dimensional reconstruction. Amelogenin mRNA was first detected in a cluster of ameloblasts along one cusp of the M1 molar at the newborn stage of development. In subsequent developmental stages, amelogenin transcripts were detected within foci of ameloblasts lining each of the five cusps comprising the molar crown form. The number of amelogenin transcripts appeared to be position-dependent, being more abundant on one cusp surface while reduced along the opposite surface. Amelogenin gene transcription was found to be bilaterally symmetric between the developing right and left M1 molars, and complementary between the M1 and M1 developing molars; indicating position-restricted gene expression resulting in organ stereoisomerism. The application of in situ hybridization to forming tooth organ geometry provides a novel strategy to define epithelial-mesenchymal signal(s) which are believed to be responsible for organ morphogenesis, as well as for temporal- and spatial-restricted tissue-specific expression of enamel extracellular matrix.

scholarly journals Wxlv, the Ancestral Allele of Rice Waxy Gene

Proceedings ◽  
2020 ◽  
Vol 36 (1) ◽  
pp. 140 ◽  
Author(s):  
Changquan Zhang ◽  
Jihui Zhu ◽  
Shengjie Chen ◽  
Qiaoquan Liu
Keyword(s):  
Amylose Content ◽  
Waxy Gene ◽  
Evolutionary Analysis ◽  
Ancestral Allele ◽  
Cultivated Rice ◽  
Functional Sites ◽  
Wx Locus ◽  
Wx Gene ◽  
Shed Light

In rice endosperms, the Waxy (Wx) gene is important for amylose synthesis, and various Wx alleles control the amylose content and affect the taste of cooked rice. Herein, we report the cloning of the ancestral allele Wxlv of the Wx locus, which affects the mouthfeel of rice grains by modulating the size of amylose molecules. Using evolutionary analysis, we demonstrated that Wxlv originated directly from wild rice, and the three major Wx alleles in cultivated rice (Wxb, Wxa, and Wxin) differentiated after the substitution of one base pair at the functional sites. These data indicate that the Wxlv allele played an important role in artificial selection and domestication. The findings also shed light on the evolution of various Wx alleles, which have greatly contributed to improving the eating and cooking quality of rice.

scholarly journals Network and Evolutionary Analysis of Human Epigenetic Regulators to Unravel Disease Associations

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1457
Author(s):  
Shinji Ohsawa ◽  
Toshiaki Umemura ◽  
Tomoyoshi Terada ◽  
Yoshinori Muto
Keyword(s):  
Positive Selection ◽  
Developmental Stages ◽  
Age Distribution ◽  
System Level ◽  
Disease Genes ◽  
Evolutionary Analysis ◽  
Distribution Analysis ◽  
Cancer Disease ◽  
High Tendency ◽  
Epigenetic Regulators

We carried out a system-level analysis of epigenetic regulators (ERs) and detailed the protein–protein interaction (PPI) network characteristics of disease-associated ERs. We found that most diseases associated with ERs can be clustered into two large groups, cancer diseases and developmental diseases. ER genes formed a highly interconnected PPI subnetwork, indicating a high tendency to interact and agglomerate with one another. We used the disease module detection (DIAMOnD) algorithm to expand the PPI subnetworks into a comprehensive cancer disease ER network (CDEN) and developmental disease ER network (DDEN). Using the transcriptome from early mouse developmental stages, we identified the gene co-expression modules significantly enriched for the CDEN and DDEN gene sets, which indicated the stage-dependent roles of ER-related disease genes during early embryonic development. The evolutionary rate and phylogenetic age distribution analysis indicated that the evolution of CDEN and DDEN genes was mostly constrained, and these genes exhibited older evolutionary age. Our analysis of human polymorphism data revealed that genes belonging to DDEN and Seed-DDEN were more likely to show signs of recent positive selection in human history. This finding suggests a potential association between positive selection of ERs and risk of developmental diseases through the mechanism of antagonistic pleiotropy.

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

Genome ◽  
2019 ◽  
Vol 62 (10) ◽  
pp. 643-656 ◽  
Author(s):  
Yong Zhou ◽  
Junjie Tao ◽  
Golam Jalal Ahammed ◽  
Jingwen Li ◽  
Youxin Yang
Keyword(s):  
Expression Analysis ◽  
Developmental Stages ◽  
Plant Responses ◽  
Distribution Analysis ◽  
Cis Elements ◽  
Promoter Regions ◽  
Specific Expression ◽  
Promoter Sequences ◽  
Genome Wide ◽  
Aquaporin Gene

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

Differential mRNA expression of the phosphoprotein p19/SCG10 gene family in mouse preimplantation embryos, uterus, and placenta

1992 ◽  
Vol 4 (2) ◽  
pp. 205 ◽  
Author(s):  
S Pampfer ◽  
W Fan ◽  
UK Schubart ◽  
JW Pollard
Keyword(s):  
Gene Family ◽  
Mammalian Cells ◽  
Developmental Stages ◽  
Blastocyst Stage ◽  
Northern Blotting ◽  
Preimplantation Embryos ◽  
Mammalian Development ◽  
Specific Expression ◽  
Developing Neurons ◽  
Early Mammalian Development

The p19/SCG10 gene family encodes two structurally related cellular proteins that are implicated in signal transduction during differentiation of mammalian cells. Previous evidence suggests that both genes are expressed in a stage-specific manner but that expression of p19 is widespread, whereas that of SCG10 is restricted to developing neurons. To determine at which developmental stage these two genes are first expressed, we have probed for mRNA transcripts in preimplantation embryos and the utero-placental unit of the mouse. As determined by polymerase chain reaction (PCR) to amplify reverse-transcribed RNA, expression of both genes was detected in preimplantation embryos, although the temporal pattern was distinct. p19 mRNA appeared transiently in 2-cell embryos, was undetectable in morulae and early blastocysts and reappeared in expanded blastocysts. In contrast, embryonic expression of SCG10 mRNA commenced in morulae and was maintained through to the blastocyst stage. Interestingly, only SCG10 expression could be detected in blastocysts derived from cultures of 2-cell embryos. During the post-implantation period, SCG10 transcripts were only detected in the uterus and placenta by reverse transcriptase-PCR, whereas p19 mRNA could be detected by Northern blotting and showed stage-specific expression in both tissues. The data confirm that, at later developmental stages, expression of p19 is widespread while that of SCG10 is more restricted. The expression of both genes in preimplantation embryos suggests distinct but possibly overlapping roles for p19 and SCG10 in early mammalian development.

scholarly journals Structural evolutionary analysis predicts functional sites in the artemisinin resistance malaria protein K13

2018 ◽  
Author(s):  
Romain Coppée ◽  
Daniel C. Jeffares ◽  
Audrey Sabbagh ◽  
Jérôme Clain
Keyword(s):  
Structural Information ◽  
Artemisinin Resistance ◽  
Evolutionary Analysis ◽  
Functional Sites ◽  
Btb Domain ◽  
Binding Surface ◽  
Species Evolution ◽  
Binding Residues ◽  
Falciparum Protein

AbstractK13 is an essential Plasmodium falciparum protein that plays a key role in malaria resistance to artemisinins. Although K13 resembles BTB- and Kelch/propeller-containing proteins involved in ubiquitin ligase complexes, its functional sites remain uncharacterized. Using evolutionary and structural information, we searched for the most conserved K13 sites across Apicomplexa species evolution to identify sub-regions of K13 that are likely functional. An amino acid electropositive ‘patch’ in the K13 propeller domain has a dense concentration of extraordinarily conserved positions located at a shallow pocket, suggesting a role as binding surface. When applied to experimentally-characterized BTB-Kelch proteins, our strategy successfully identifies the validated substrate-binding residues within their own propeller shallow pocket. Another patch of slowly evolving sites is identified in the K13 BTB domain which partially overlaps the surface that binds to Cullin proteins in BTB-Cullin complexes. We provide candidate binding sites in K13 propeller and BTB domains for functional follow-up studies.

scholarly journals Genome-wide survey and expression analysis of the SLAC/SLAH gene family in pear (Pyrus bretschneideri) and other members of the Rosaceae

2018 ◽  
Author(s):  
Guodong Chen ◽  
Xiaolong Li ◽  
Xin qiao ◽  
Jiaming Li ◽  
Li Wang ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Prunus Persica ◽  
Higher Plants ◽  
Chloride Transport ◽  
Structural Characteristics ◽  
Evolutionary Analysis ◽  
Anion Channels ◽  
Genome Wide ◽  
A Genome

AbstractS-type anion channels (SLAC/SLAHs), which play important roles in plant anion (such as nitrate and chloride) transport, growth and development, abiotic stress responses and hormone signaling. However, there is far less information about this family in Rosaceae species. We performed a genome-wide analysis and identified SLAC/SLAH gene family members in pear (Pyrus bretschneideri) and four other species of Rosaceae (Malus domestica, Prunus persica, Fragaria vesca and Prunus mume). A total of 21 SLAC/SLAH genes were identified from the five Rosaceae species. Based on the structural characteristics and a phylogenetic analysis of these genes, the SLAC/SLAH gene family could be classified into three main groups (I, II and III). The evolutionary analysis showed that the SLAC/SLAH gene family was comparatively conserved during the evolution of Rosaceae species. Transcriptome data demonstrated that PbrSLAC/SLAH genes were detected in all parts of the pear. However, PbrSLAC1 showed a higher expression level in leaf, while PbrSLAH2/3 was mainly expressed in roots. In addition, PbrSLAC/SLAH genes were only located on the plasma membrane in transient expression experiments in Arabidopsis protoplasts cells. These results provide valuable information that increases our understanding of the evolution, expression and functions of the SLAC/SLAH gene family in higher plants.

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