What can the phylogeny of class I KNOX genes and their expression patterns in land plants tell us about the evolution of shoot development?

2021 ◽  
Author(s):  
Anastasiia I Maksimova ◽  
Lidija Berke ◽  
Marco G Salgado ◽  
Ekaterina A Klimova ◽  
Katharina Pawlowski ◽  
...  
Keyword(s):  
Cell Differentiation ◽  
Leaf Shape ◽  
Expression Patterns ◽  
Gene Families ◽  
Class Ii ◽  
Leaf Primordium ◽  
Land Plants ◽  
Class I ◽  
Knox Gene ◽  
Knox Genes

Abstract KNOX genes encode transcription factors (TFs), several of which act non-cell-autonomously. KNOX genes evolved in algae, and two classes, class I KNOX and class II KNOX genes, were already present in charophytes. In tracheophytes, class I KNOX genes are expressed in shoot apical meristems (SAMs) and thought to inhibit cell differentiation, whereas class II KNOX genes are expressed in mature organs regulating differentiation. In this review, we summarize the data available on gene families and expression patterns of class I and class II KNOX genes in embryophytes. The expression patterns of class I KNOX genes should be seen in the context of SAM structure and of leaf primordium development where the inhibition of cell differentiation needs to be lifted. Although the SAMs of angiosperms and gnetophytes almost always belong to the duplex type, several other types are distributed in gymnosperms, ferns, lycopods and bryophytes. KNOX gene families remained small (maximally five genes) in the representatives of bryophytes, lycopods and ferns examined thus far; however, they expanded to some extent in gymnosperms and, independently and much more strongly, in angiosperms. The growing sophistication of mechanisms to repress and re-induce class KNOX I expression played a major role in the evolution of leaf shape.

scholarly journals Extended expression of MaKN1 contributes to the leaf morphology in aquatic forms of Myriophyllum aquaticum

Botany ◽  
2015 ◽  
Vol 93 (9) ◽  
pp. 611-621
Author(s):  
M.D. Shafiullah ◽  
Christian R. Lacroix
Keyword(s):  
Apical Meristem ◽  
Leaf Morphology ◽  
Expression Patterns ◽  
Homeobox Gene ◽  
Leaf Primordia ◽  
Leaf Primordium ◽  
Myriophyllum Aquaticum ◽  
Knox Gene ◽  
Leaf Morphogenesis

Myriophyllum aquaticum (Vell.) Verdc. is heterophyllous in nature with highly dissected simple leaves consisting of several lobes. KNOX (KNOTTED1-LIKE HOMEOBOX) genes are believed to have played an important role in the evolution of leaf diversity. Up-regulation of KNOX during leaf primordium initiation can lead to leaf dissection in plants with simple leaves and, if overexpressed, can produce ectopic meristems on leaves. A previous study on KNOX gene expression in the aerial form of this species showed that this gene is expressed in the shoot apical meristem (SAM), as well as in leaf primordia P0 to P8. Based on these results, it was hypothesized that the prolonged expression of the MaKN1 (Myriophyllum aquaticum Knotted1-like homeobox) gene beyond P8, might play an important role in the generation of more lobes, longer lobes, and hydathode formation in the aquatic leaves of M. aquaticum. The technique of in situ hybridization was carried out using a previously sequenced 300 bp fragment of MaKN1 to determine the expression patterns of this gene in the shoot of aquatic forms of the plant. Expression patterns of MaKN1 revealed that the SAM and leaf primordia of aquatic forms of M. aquaticum at levels P0 (youngest) to P4 were distributed throughout these structures. The level of expression of this MaKN1 gene progressively became more localized to lobes in older leaf primordia (levels P5 to P12). Previous studies of aerial forms of this plant showed MaKN1 expression until P8. Our results with aquatic forms show that the highly dissected leaf morphology in aquatic forms was the result of the prolonged expression of MaKN1 beyond P8. This resulted in the formation of elongated and slightly more numerous lobes, and hydathodes in aquatic forms. These findings support the view that KNOX genes are important developmental regulators of leaf morphogenesis and have played an important role in the evolution of leaf forms in the plant kingdom.

scholarly journals Transcriptome and DNA Methylation Analyses of the Molecular Mechanisms Underlying with Longissimus dorsi Muscles at Different Stages of Development in the Polled Yak

Genes ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 970 ◽  
Author(s):  
Ma ◽  
Jia ◽  
Chu ◽  
Fu ◽  
Lei ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Methylation Status ◽  
Muscle Growth ◽  
Class Ii ◽  
Epigenetic Mechanism ◽  
Class I ◽  
Longissimus Dorsi ◽  
Growth Stages

DNA methylation modifications are implicated in many biological processes. As the most common epigenetic mechanism DNA methylation also affects muscle growth and development. The majority of previous studies have focused on different varieties of yak, but little is known about the epigenetic regulation mechanisms in different age groups of animals. The development of muscles in the different stages of yak growth remains unclear. In this study, we selected the longissimus dorsi muscle tissue at three different growth stages of the yak, namely, 90-day-old fetuses (group E), six months old (group M), and three years old (group A). Using RNA-Seq transcriptome sequencing and methyl-RAD whole-genome methylation sequencing technology, changes in gene expression levels and DNA methylation status throughout the genome were investigated during the stages of yak development. Each group was represented by three biological replicates. The intersections of expression patterns of 7694 differentially expressed genes (DEGs) were identified (padj < 0.01, |log2FC| > 1.2) at each of the three developmental periods. Time-series expression profile clustering analysis indicated that the DEGs were significantly arranged into eight clusters which could be divided into two classes (padj < 0.05), class I profiles that were downregulated and class II profiles that were upregulated. Based on this cluster analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that DEGs from class I profiles were significantly (padj < 0.05) enriched in 21 pathways, the most enriched pathway being the Axon guidance signaling pathway. DEGs from the class II profile were significantly enriched in 58 pathways, the pathway most strongly enriched being Metabolic pathway. After establishing the methylation profiles of the whole genomes, and using two groups of comparisons, the three combinations of groups (M-vs.-E, M-vs.-A, A-vs.-E) were found to have 1344, 822, and 420 genes, respectively, that were differentially methylated at CCGG sites and 2282, 3056, and 537 genes, respectively, at CCWGG sites. The two sets of data were integrated and the negative correlations between DEGs and differentially methylated promoters (DMPs) analyzed, which confirmed that TMEM8C, IGF2, CACNA1S and MUSTN1 were methylated in the promoter region and that expression of the modified genes was negatively correlated. Interestingly, these four genes, from what was mentioned above, perform vital roles in yak muscle growth and represent a reference for future genomic and epigenomic studies in muscle development, in addition to enabling marker-assisted selection of growth traits.

Transgenic lines of Begonia maculata generated by ectopic expression of PttKN1

Biologia ◽  
2011 ◽  
Vol 66 (2) ◽  
Author(s):  
Quan-le Xu ◽  
Jiang-ling Dong ◽  
Nan Gao ◽  
Mei-yu Ruan ◽  
Hai-yan Jia ◽  
...  
Keyword(s):  
Transgenic Plants ◽  
Ectopic Expression ◽  
Class I ◽  
Wild Type Plant ◽  
Wild Type ◽  
Knox Gene ◽  
Knox Genes ◽  
Pttkn1 Gene ◽  
Transgenic Lines ◽  
First Time

AbstractKNOX (KNOTTED1-like homeobox) genes encode homeodomain-containing transcription factors which play crucial roles in meristem maintenance and proper patterning of organ initiation. PttKN1 gene, isolated from the vascular cambium of hybrid aspen (Populus tremula × P. tremuloides), is a member of class I KNOX gene family. In order to understand the roles of PttKN1 gene in meristem activity and morphogenesis as well as to explore the possibility to generate novel ornamental lines via its ectopic expression, it was introduced into the genome of Begonia maculata Raddi by Agrobacterium tumefasciens-mediated gene transformation here. Four types of transgenic plants were observed, namely coral-like (CL) type, ectopic foliole (EF) type, phyllotaxy-irregular (IP) type and cup-shaped (CS) type, which were remarkably different from corresponding wild type and were not also observed in the regenerated plantlets of wild type plant. Among these four types of transgenic plants, the phenotype of coral-like was observed for the first time in the transformants ectopically expressed KNOX genes. The observation of scanning electron microscope (SEM) showed ectopic meristems on the adaxial leaf surface of the transformants. Interestingly, the plantlets with ectopic foliole could generate new ectopic folioles from the original ectopic folioles again, and the plants regenerated from the EF-type transformants could also maintain the original morphology. The same specific RT-PCR band of the four types of transgenic plantlets showed that PttKN1 was ectopically expressed. All these data demonstrated that the ectopic expression of PttKN1 caused a series of alterations in morphology which provided possibilities producing novel ornamental lines and that PttKN1 played important roles in meristem initiation, maintenance and organogenesis events as other class I KNOX genes.

scholarly journals Genome-wide identification and expression analysis of the trehalose-6-phosphate synthase (TPS) gene family in cucumber (Cucumis sativus L.)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11398
Author(s):  
Yuanyuan Dan ◽  
Yuan Niu ◽  
Chunlei Wang ◽  
Mei Yan ◽  
Weibiao Liao
Keyword(s):  
Expression Analysis ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Light Response ◽  
Class Ii ◽  
Class I ◽  
Motif Analysis ◽  
Cucumis Sativus L ◽  
Conserved Motifs ◽  
Phosphate Synthase

Trehalose-6-phosphate synthase (TPS) is significant in the growth, development and stress resistance of plants. We identified the cucumber TPS family and its physicochemical properties, domains, gene structures, evolutionary relationships, gene locations, cis-acting elements, conserved motifs, and expression patterns using bioinformatics. Our results uncovered seven CsTPS genes in the cucumber genome and named CsTPS1–CsTPS7 according to their locations in the chromosomes. Seven CsTPS genes were randomly distributed in six cucumber chromosomes. Domain analysis showed that the TPS and TPP domains exist in all CsTPSs, and an additional hydrolase-3 domain exist in CsTPS3, CsTPS5 and CsTPS6. Phylogenetic analysis showed that TPS proteins from Arabidopsis, rice, soybean, and cucumber were divided into two subfamilies (Class I and Class II) and they were further divided into seven subgroups. TPS proteins from Arabidopsis and cucumber were grouped together, suggesting a close evolutionary relationship. Gene structure analysis indicated that most Class I genes contained 16–17 introns, while Class II genes (except CsTPS7) had two introns. Motif analysis showed that Class II genes had 10 complete conserved motifs, while Class I genes lacked motif 8 and motif 9. Furthermore, CsTPS genes possessed numerous cis-acting elements related to stress, hormone, and light response in the promoter regions. GO analysis indicated multiple functions for the CsTPS proteins. Expression analysis of CsTPS genes in different tissues found that they were expressed in roots, stems and leaves, with the highest expression levels in roots. The expression analysis of CsTPSs under different treatments showed that CsTPS genes may participate in the response to abiotic stress, plant hormones and sugar treatments.

scholarly journals CLASS-II KNOX genes coordinate spatial and temporal patterns of the tomato ripening

2021 ◽  
Author(s):  
Alexandra Keren-Keiserman ◽  
Amit Shtern ◽  
Daniel Chalupowicz ◽  
Chihiro Furumizu ◽  
John p Alvarez ◽  
...  
Keyword(s):  
Developmental Change ◽  
Tomato Fruit ◽  
Temporal Patterns ◽  
Class Ii ◽  
Knox Gene ◽  
Spatial And Temporal Patterns ◽  
Knox Genes ◽  
Leaf Phenotype ◽  
Tomato Fruit Ripening ◽  
Transcriptional Changes

Ripening is a complex developmental change of a mature organ, the fruit. In plants like a tomato, it involves softening, pigmentation, and biosynthesis of metabolites beneficial for the human diet. Examination of the transcriptional changes towards ripening suggests that redundant uncharacterized factors may be involved in the coordination of the ripening switch. Previous studies have demonstrated that Arabidopsis CLASS-II KNOX genes play a significant role in controlling the maturation of siliques and their transition to senescence. Here we examined the combined role of all four tomato CLASS-II KNOX genes in the maturation and ripening of fleshy fruits using an artificial microRNA targeting them simultaneously. As expected, the knockdown plants (35S::amiR-TKN-CL-II) exhibited leaves with increased complexity, reminiscent of the leaf phenotype of plants overexpressing CLASS- I KNOX, which antagonize CLASS-II KNOX gene functions. The fruits of 35S::amiR-TKN-CL-II plants were notably smaller than the control. While their internal gel/placenta tissue softened and accumulated the typical pigmentation, the pericarp color break took place ten days later than control, and eventually, it turned yellow instead of red. Additionally, the pericarp of 35S::amiR-TKN-CL-II fruits remained significantly firmer than control even after three weeks of shelf storage. Strikingly, the 35S::amiR-TKN-CL-II fruits showed early ethylene release and respiration peak, but these were correlated only with liquefaction and pigmentation of the internal tissues. Our findings suggest that CLASS-II KNOX genes are required to coordinate the spatial and temporal patterns of tomato fruit ripening.

AML1-ETO Collaborates with the TALE Homeobox Genes MEIS1 and MEIS2 in Inducing AML.

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 2387-2387
Author(s):  
Naidu M Vegi ◽  
Josef Klappacher ◽  
Franz Oswald ◽  
Rainer Claus ◽  
Medhanie M Mulaw ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Cell Lines ◽  
Conflicts Of Interest ◽  
Expression Patterns ◽  
Homeobox Genes ◽  
Class Ii ◽  
Class I ◽  
Control Group ◽  
Murine Bone Marrow ◽  
Functional Relevance

Abstract Abstract 2387 AML1-ETO (AE) is the most frequent fusion gene in human AML. Previously, we and others have demonstrated that the fusion is not able to cause leukemia on its own in experimental murine models, but that it needs collaborative partners. Following the ‘two-hit model’ hypothesis that class I and class II mutations have to collaborate to induce leukemia, we could previously demonstrate that AE (class II) collaborates with FLT3-length mutation (class I) to generate AML in the murine bone marrow transplantation model (BMT model). We now demonstrate that AE can collaborate with mutations of its own class in inducing AML. We focussed our analyses on the TALE homeobox gene family, namely Meis1 and Meis2, as already known in the case of Meis1 to be a potent co-factor for Hox gene associated leukemias and being classified as other homeobox genes as a class II mutation. First, real-time RT - PCR confirmed that MEIS1 is expressed at high levels in a subgroup of AE positive AML patients. Furthermore, MEIS2 was highly and aberrantly expressed virtually in all AE patients (n=70) compared to normal bone marrow. Expression patterns of both MEIS genes correlated with their promoter methylation in the t(8;21) patients and cell lines. To test the functional relevance of MEIS expression in human AE patients, we analysed collaboration of AE with Meis genes in the BMT model: Meis1 and Meis2 were retrovirally expressed alone or in combination with AE in 5-FU treated primary murine bone marrow and injected into lethally irradiated recipients (AML1-ETO alone, n=10; EGFP control, n=7; AE+Meis1, n=14; AE+Meis2, n=4). None of the mice in the AE as well as in the control group developed disease. In contrast, mice transplanted with BM co-expressing AE+Meis1 and AE+Meis2 developed lethal disease after a median latency of 102 and 255 days respectively. AE+Meis1 induced MPS in three, AML in seven and ALL in three cases, whereas AE+Meis2 induced AML in all cases. Functional relevance of MEIS expression was further confirmed in human AML cell lines as shRNA mediated depletion of MEIS1 as well as MEIS2 impaired cell growth in AE positive AML cell lines and so far one primary AE AML sample. To understand the mechanisms of AE/MEIS collaboration co-immunoprecipitation assays were performed documenting weak binding of Meis1, but strong interaction of Meis2 with AE. ChIP-Seq is currently being performed to test whether DNA binding of MEIS genes alter in collaboration with AE. Taken together, we could demonstrate that AE collaborates with Meis genes in AML. It furthermore shows that a class II mutation can be converted into an overt oncogene by a mutation of its own class. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Genome-Wide Analysis of the TCP Transcription Factor Genes in Dendrobium catenatum Lindl.

2021 ◽  
Vol 22 (19) ◽  
pp. 10269
Author(s):  
Li Zhang ◽  
Cheng Li ◽  
Danni Yang ◽  
Yuhua Wang ◽  
Yongping Yang ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Class Ii ◽  
Class I ◽  
Genome Wide Analysis ◽  
Cell Proliferation And Differentiation ◽  
Genome Wide ◽  
A Genome ◽  
Transcription Factor Genes ◽  
Transient Activity

Teosinte branched1/cycloidea/proliferating cell factor (TCP) gene family members are plant-specific transcription factors that regulate plant growth and development by controlling cell proliferation and differentiation. However, there are no reported studies on the TCP gene family in Dendrobium catenatum Lindl. Here, a genome-wide analysis of TCP genes was performed in D. catenatum, and 25 TCP genes were identified. A phylogenetic analysis classified the family into two clades: Class I and Class II. Genes in the same clade share similar conserved motifs. The GFP signals of the DcaTCP-GFPs were detected in the nuclei of tobacco leaf epidermal cells. The activity of DcaTCP4, which contains the miR319a-binding sequence, was reduced when combined with miR319a. A transient activity assay revealed antagonistic functions of Class I and Class II of the TCP proteins in controlling leaf development through the jasmonate-signaling pathway. After different phytohormone treatments, the DcaTCP genes showed varied expression patterns. In particular, DcaTCP4 and DcaTCP9 showed opposite trends after 3 h treatment with jasmonate. This comprehensive analysis provides a foundation for further studies on the roles of TCP genes in D. catenatum.

The rough sheath2 gene negatively regulates homeobox gene expression during maize leaf development

Development ◽  
1998 ◽  
Vol 125 (15) ◽  
pp. 2857-2865 ◽  
Author(s):  
R. Schneeberger ◽  
M. Tsiantis ◽  
M. Freeling ◽  
J.A. Langdale
Keyword(s):  
Gene Expression ◽  
Cell Fate ◽  
Higher Plants ◽  
Leaf Shape ◽  
Ectopic Expression ◽  
Homeobox Gene ◽  
Current Evidence ◽  
Leaf Cell ◽  
Knox Gene ◽  
Knox Genes

Leaves of higher plants are produced in a sequential manner through the differentiation of cells that are derived from the shoot apical meristem. Current evidence suggests that this transition from meristematic to leaf cell fate requires the down-regulation of knotted1-like homeobox (knox) gene expression. If knox gene expression is not repressed, overall leaf shape and cellular differentiation within the leaf are perturbed. In order to identify genes that are required for the aquisition of leaf cell fates, we have genetically screened for recessive mutations that confer phenotypes similar to dominant mutations (e.g. Knotted1 and Rough sheath1) that result in the ectopic expression of class I knox genes. Independently derived mutations at the rough sheath2 (rs2) locus condition a range of pleiotropic leaf, node and internode phenotypes that are sensitive to genetic background and environment. Phenotypes include dwarfism, leaf twisting, disorganized differentiation of the blade-sheath boundary, aberrant vascular patterning and the generation of semi-bladeless leaves. knox genes are initially repressed in rs2 mutants as leaf founder cells are recruited in the meristem. However, this repression is often incomplete and is not maintained as the leaf progresses through developement. Expression studies indicate that three knox genes are ectopically or over-expressed in developing primordia and in mature leaves. We therefore propose that the rs2 gene product acts to repress knox gene expression (either directly or indirectly) and that rs2 gene action is essential for the elaboration of normal leaf morphology.

scholarly journals Molecular evolution and expression divergence of three key Met biosynthetic genes in plants: CGS, HMT and MMT

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e6023 ◽  
Author(s):  
Man Zhao ◽  
Wenyi Wang ◽  
Lei Wei ◽  
Peng Chen ◽  
Fengjie Yuan ◽  
...  
Keyword(s):  
Biosynthetic Pathway ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Evolutionary Model ◽  
Gene Families ◽  
Land Plants ◽  
Seed Plants ◽  
Class 1 ◽  
Food And Feed ◽  
Relationship Of

Methionine (Met) is an essential sulfur-containing amino acid in animals. Cereal and legume crops with limiting levels of Met represent the major food and feed sources for animals. In plants, cystathionine gamma-synthase (CGS), methionine methyltransferase (MMT) and homocysteine methyltransferase (HMT) are committing enzymes synergistically synthesizing Met through the aspartate (Asp) family pathway and the S-methylmethionine (SMM) cycle. The biological functions of CGS, MMT and HMT genes have been respectively studied, whereas their evolution patterns and their contribution to the evolution of Met biosynthetic pathway in plants are unknown. In the present study, to reveal their evolution patterns and contribution, the evolutionary relationship of CGS, MMT and HMT gene families were reconstructed. The results showed that MMTs began in the ancestor of the land plants and kept conserved during evolution, while the CGSs and HMTs had diverged. The CGS genes were divided into two branches in the angiosperms, Class 1 and Class 2, of which Class 2 only contained the grasses. However, the HMT genes diverged into Class 1 and Class 2 in all of the seed plants. Further, the gene structure analysis revealed that the CGSs, MMTs and HMTs were relatively conserved except for the CGSs in Class 2. According to the expression of CGS, HMT and MMT genes in soybeans, as well as in the database of soybean, rice and Arabidopsis, the expression patterns of the MMTs were shown to be consistently higher in leaves than in seeds. However, the expression of CGSs and HMTs had diverged, either expressed higher in leaves or seeds, or showing fluctuated expression. Additionally, the functions of HMT genes had diverged into the repair of S-adenosylmethionine and SMM catabolism during the evolution. The results indicated that the CGS and HMT genes have experienced partial subfunctionalization. Finally, given the evolution and expression of the CGS, HMT and MMT gene families, we built the evolutionary model of the Met biosynthetic pathways in plants. The model proposed that the Asp family pathway existed in all the plant lineages, while the SMM cycle began in the ancestor of land plants and then began to diverge in the ancestor of seed plants. The model suggested that the evolution of Met biosynthetic pathway is basically consistent with that of plants, which might be vital to the growth and development of different botanical lineages during evolution.

Electron microscopy analysis of degenerating pancreatic ß cells in transgenic mice expressing the MHC Class I antigen Dd

1990 ◽  
Vol 48 (3) ◽  
pp. 548-549
Author(s):  
T. A. Stewart ◽  
D. Liggitt ◽  
S. Pitts ◽  
L. Martin ◽  
M. Siegel ◽  
...  
Keyword(s):  
Type I Diabetes ◽  
Disease Process ◽  
Class Ii ◽  
Class I ◽  
Type I ◽  
Aberrant Expression ◽  
Mhc Molecules ◽  
Endogenous Insulin ◽  
Class Ii Mhc ◽  
Ifn Γ

Insulin-dependant (Type I) diabetes mellitus (IDDM) is a metabolic disorder resulting from the lack of endogenous insulin secretion. The disease is thought to result from the autoimmune mediated destruction of the insulin producing ß cells within the islets of Langerhans. The disease process is probably triggered by environmental agents, e.g. virus or chemical toxins on a background of genetic susceptibility associated with particular alleles within the major histocompatiblity complex (MHC). The relation between IDDM and the MHC locus has been reinforced by the demonstration of both class I and class II MHC proteins on the surface of ß cells from newly diagnosed patients as well as mounting evidence that IDDM has an autoimmune pathogenesis. In 1984, a series of observations were used to advance a hypothesis, in which it was suggested that aberrant expression of class II MHC molecules, perhaps induced by gamma-interferon (IFN γ) could present self antigens and initiate an autoimmune disease. We have tested some aspects of this model and demonstrated that expression of IFN γ by pancreatic ß cells can initiate an inflammatory destruction of both the islets and pancreas and does lead to IDDM.

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