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.

scholarly journals Comprehensive Analysis of the Histone Deacetylase Gene Family in Chinese Cabbage (Brassica rapa): From Evolution and Expression Pattern to Functional Analysis of BraHDA3

Agriculture ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 244
Author(s):  
Seung Hee Eom ◽  
Tae Kyung Hyun
Keyword(s):  
Functional Analysis ◽  
Brassica Rapa ◽  
Chinese Cabbage ◽  
Stress Responses ◽  
Histone Deacetylases ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Gene Families ◽  
Physiological Processes ◽  
Lysine Residues

Histone deacetylases (HDACs) are known as erasers that remove acetyl groups from lysine residues in histones. Although plant HDACs play essential roles in physiological processes, including various stress responses, our knowledge concerning HDAC gene families and their evolutionary relationship remains limited. In Brassica rapa genome, we identified 20 HDAC genes, which are divided into three major groups: RPD3/HDA1, HD2, and SIR2 families. In addition, seven pairs of segmental duplicated paralogs and one pair of tandem duplicated paralogs were identified in the B. rapa HDAC (BraHDAC) family, indicating that segmental duplication is predominant for the expansion of the BraHDAC genes. The expression patterns of paralogous gene pairs suggest a divergence in the function of BraHDACs under various stress conditions. Furthermore, we suggested that BraHDA3 (homologous of Arabidopsis HDA14) encodes the functional HDAC enzyme, which can be inhibited by Class I/II HDAC inhibitor SAHA. As a first step toward understanding the epigenetic responses to environmental stresses in Chinese cabbage, our results provide a solid foundation for functional analysis of the BraHDAC family.

scholarly journals Identification, Evolutionary and Expression Analysis of PYL-PP2C-SnRK2s Gene Families in Soybean

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1356
Author(s):  
Zhaohan Zhang ◽  
Shahid Ali ◽  
Tianxu Zhang ◽  
Wanpeng Wang ◽  
Linan Xie
Keyword(s):  
Gene Family ◽  
Higher Plants ◽  
Expression Patterns ◽  
Family Members ◽  
Evolutionary Relationship ◽  
Gene Families ◽  
Class Iii ◽  
Sequencing Data ◽  
Entire Genome ◽  
Core Components

Abscisic acid (ABA) plays a crucial role in various aspects of plant growth and development, including fruit development and ripening, seed dormancy, and involvement in response to various environmental stresses. In almost all higher plants, ABA signal transduction requires three core components; namely, PYR/PYL/RCAR ABA receptors (PYLs), type 2C protein phosphatases (PP2Cs), and class III SNF-1-related protein kinase 2 (SnRK2s). The exploration of these three core components is not comprehensive in soybean. This study identified the GmPYL-PP2C-SnRK2s gene family members by using the JGI Phytozome and NCBI database. The gene family composition, conservation, gene structure, evolutionary relationship, cis-acting elements of promoter regions, and its coding protein domains were analyzed. In the entire genome of the soybean, there are 21 PYLs, 36 PP2Cs, and 21 SnRK2s genes; further, by phylogenetic and conservation analysis, 21 PYLs genes are classified into 3 groups, 36 PP2Cs genes are classified into seven groups, and 21 SnRK2s genes are classified into 3 groups. The conserved motifs and domain analysis showed that all the GmPYLs gene family members contain START-like domains, the GmPP2Cs gene family contains PP2Cc domains, and the GmSnRK2s gene family contains S_TK domains, respectively. Furthermore, based on the high-throughput transcriptome sequencing data, the results showed differences in the expression patterns of GmPYL-PP2C-SnRK2s gene families in different tissue parts of the same variety, and the same tissue part of different varieties. Our study provides a basis for further elucidation of the identification of GmPYL-PP2C-SnRK2s gene family members and analysis of their evolution and expression patterns, which helps to understand the molecular mechanism of soybean response to abiotic stress. In addition, this provides a conceptual basis for future studies of the soybean ABA core signal pathway.

scholarly journals Role of Ethylene in the Biosynthetic Pathway of Related-aroma Volatiles Derived from Fatty Acids in Oriental Sweet Melon

2016 ◽  
Vol 141 (4) ◽  
pp. 327-338 ◽  
Author(s):  
Yan Li ◽  
Hongyan Qi ◽  
Yazhong Jin ◽  
Xiaobin Tian ◽  
Linlin Sui ◽  
...  
Keyword(s):  
Volatile Compounds ◽  
Biosynthetic Pathway ◽  
Expression Patterns ◽  
Gene Families ◽  
Hydroperoxide Lyase ◽  
Straight Chain ◽  
Alcohol Acetyltransferase ◽  
Key Enzyme ◽  
Aroma Precursors

The catabolism of fatty acid (FA) is regarded as a key pathway of aroma volatile compounds in oriental sweet melon (Cucumis melo var. makuwa). In our research, two cultivars of oriental sweet melon, Caihong7 and Tianbao, were employed to illuminate which step of the biosynthetic pathway of aroma compounds could be regulated by ethylene (ETH). The role of ETH in determining the profiles of straight-chain aroma volatile compounds, levels of FA as aroma precursors, activities of aroma-related enzymes derived from FA pathway, and expression patterns of key enzymes were investigated. Overall, exogenous application of ETH increased the production rates of endogenous ETH and levels of FA. Compared with control, the level of straight-chain esters, especially the acetate, hexanoate, and hexyl esters, was significantly increased by ETH, whereas the content of alcohol and aldehyde reduced. In addition, the metabolism of free FA included linoleic acid (LA), linolenic acid (LeA), and oleic acid (OA) appeared to be ETH-dependent. The activities of lipoxygenase (LOX), alcohol dehydrogenase (ADH), and alcohol acetyltransferase (AAT) as well as the expression patterns of Cm-ADH1, Cm-ADH2, Cm-AAT1, and Cm-AAT4 were positively regulated by ETH. In contrast, hydroperoxide lyase (HPL) and Cm-AAT2 and Cm-AAT3 seemed to be independent of ETH modulation. These results suggested that the dissimilation of FA included LA, LeA, and OA into the acetate, hexanoate, and hexyl esters mainly through ETH regulating the LOX pathway by enhancing the expression of particular members of aroma-related key enzyme gene families as well as the activities of dehydrogenation and esterification.

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 Genome-wide identification, evolutionary relationship and expression analysis of AGO, DCL and RDR family genes in tea

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Debasish B. Krishnatreya ◽  
Pooja Moni Baruah ◽  
Bhaskar Dowarah ◽  
Soni Chowrasia ◽  
Tapan Kumar Mondal ◽  
...  
Keyword(s):  
Expression Analysis ◽  
Small Rna ◽  
Expression Patterns ◽  
Crop Improvement ◽  
Evolutionary Relationship ◽  
Constitutive Expression ◽  
Gene Families ◽  
Tea Plant ◽  
Variable Expression ◽  
Genome Wide

AbstractThree gene families in plants viz. Argonaute (AGOs), Dicer-like (DCLs) and RNA dependent RNA polymerase (RDRs) constitute the core components of small RNA mediated gene silencing machinery. The present study endeavours to identify members of these gene families in tea and to investigate their expression patterns in different tissues and various stress regimes. Using genome-wide analysis, we have identified 18 AGOs, 5 DCLs and 9 RDRs in tea, and analyzed their phylogenetic relationship with orthologs of Arabidopsis thaliana. Gene expression analysis revealed constitutive expression of CsAGO1 in all the studied tissues and stress conditions, whereas CsAGO10c showed most variable expression among all the genes. CsAGO10c gene was found to be upregulated in tissues undergoing high meristematic activity such as buds and roots, as well as in Exobasidium vexans infected samples. CsRDR2 and two paralogs of CsAGO4, which are known to participate in biogenesis of hc-siRNAs, showed similarities in their expression levels in most of the tea plant tissues. This report provides first ever insight into the important gene families involved in biogenesis of small RNAs in tea. The comprehensive knowledge of these small RNA biogenesis purveyors can be utilized for tea crop improvement aimed at stress tolerance and quality enhancement.

Phylogeny of actin and tubulin gene homologs in diverse eukaryotic species

2019 ◽  
Vol 79 (01S) ◽  
Author(s):  
Pawan Kumar Jayaswal ◽  
Asheesh Shanker ◽  
Nagendra Kumar Singh
Keyword(s):  
Evolutionary Relationship ◽  
Genomic Data ◽  
Gene Clusters ◽  
Species Trees ◽  
Model Species ◽  
Tubulin Gene ◽  
Tubulin Genes ◽  
Eukaryotic Species ◽  
Relationship Of ◽  
Insight Into

Actin and tubulin are cytoskeleton proteins, which are important components of the celland are conserved across species. Despite their crucial significance in cell motility and cell division the distribution and phylogeny of actin and tubulin genes across taxa is poorly understood. Here we used publicly available genomic data of 49 model species of plants, animals, fungi and Protista for further understanding the distribution of these genes among diverse eukaryotic species using rice as reference. The highest numbers of rice actin and tubulin gene homologs were present in plants followed by animals, fungi and Protista species, whereas ten actin and nine tubulin genes were conserved in all 49 species. Phylogenetic analysis of 19 actin and 18 tubulin genes clustered them into four major groups each. One each of the actin and tubulin gene clusters was conserved across eukaryotic species. Species trees based on the conserved actin and tubulin genes showed evolutionary relationship of 49 different taxa clustered into plants, animals, fungi and Protista. This study provides a phylogenetic insight into the evolution of actin and tubulin genes in diverse eukaryotic species.

scholarly journals Functional examination of lncRNAs in allotetraploid Gossypium hirsutum

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Luyao Wang ◽  
Jin Han ◽  
Kening Lu ◽  
Menglin Li ◽  
Mengtao Gao ◽  
...  
Keyword(s):  
Abiotic Stresses ◽  
Expression Patterns ◽  
Leaf Tissue ◽  
Evolutionary Model ◽  
Cotton Leaf ◽  
Functional Screening ◽  
Virus Induced Gene Silencing ◽  
Individual Gene ◽  
Cotton Species ◽  
Allotetraploid Cotton

Abstract Background An evolutionary model using diploid and allotetraploid cotton species identified 80 % of non-coding transcripts in allotetraploid cotton as being uniquely activated in comparison with its diploid ancestors. The function of the lncRNAs activated in allotetraploid cotton remain largely unknown. Results We employed transcriptome analysis to examine the relationship between the lncRNAs and mRNAs of protein coding genes (PCGs) in cotton leaf tissue under abiotic stresses. LncRNA expression was preferentially associated with that of the flanking PCGs. Selected highly-expressed lncRNA candidates (n = 111) were subjected to a functional screening pilot test in which virus-induced gene silencing was integrated with abiotic stress treatment. From this low-throughput screen, we obtained candidate lncRNAs relating to plant height and tolerance to drought and other abiotic stresses. Conclusions Low-throughput screen is an effective method to find functional lncRNA for further study. LncRNAs were more active in abiotic stresses than PCG expression, especially temperature stress. LncRNA XLOC107738 may take a cis-regulatory role in response to environmental stimuli. The degree to which lncRNAs are constitutively expressed may impact expression patterns and functions on the individual gene level rather than in genome-wide aggregate.

scholarly journals A Comprehensive Phylogenetic and Bioinformatics Survey of Lectins in the Fungal Kingdom

2021 ◽  
Vol 7 (6) ◽  
pp. 453
Author(s):  
Annie Lebreton ◽  
François Bonnardel ◽  
Yu-Cheng Dai ◽  
Anne Imberty ◽  
Francis M. Martin ◽  
...  
Keyword(s):  
Evolutionary Relationship ◽  
Large Family ◽  
Gene Families ◽  
Carbohydrate Binding ◽  
Sequence Motifs ◽  
Fungal Lectin ◽  
Quaternary Structures ◽  
High Degree ◽  
Carbohydrate Ligand ◽  
Fungal Kingdom

Fungal lectins are a large family of carbohydrate-binding proteins with no enzymatic activity. They play fundamental biological roles in the interactions of fungi with their environment and are found in many different species across the fungal kingdom. In particular, their contribution to defense against feeders has been emphasized, and when secreted, lectins may be involved in the recognition of bacteria, fungal competitors and specific host plants. Carbohydrate specificities and quaternary structures vary widely, but evidence for an evolutionary relationship within the different classes of fungal lectins is supported by a high degree of amino acid sequence identity. The UniLectin3D database contains 194 fungal lectin 3D structures, of which 129 are characterized with a carbohydrate ligand. Using the UniLectin3D lectin classification system, 109 lectin sequence motifs were defined to screen 1223 species deposited in the genomic portal MycoCosm of the Joint Genome Institute. The resulting 33,485 putative lectin sequences are organized in MycoLec, a publicly available and searchable database. These results shed light on the evolution of the lectin gene families in fungi.

scholarly journals Identification and Functional Analysis of a Lysozyme Gene from Coridius Chinensis (Hemiptera: Dinidoridae)

Biology ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 330
Author(s):  
Hai Huang ◽  
Juan Du ◽  
Shang-Wei Li ◽  
Tao Gong
Keyword(s):  
Innate Immunity ◽  
Fat Body ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Immune Defense ◽  
Amino Acid Residues ◽  
Immune Effector ◽  
Medicinal Value ◽  
Muramidase Activity ◽  
Insect Innate Immunity

Coridius chinensis is a valuable medicinal insect resource in China. Previous studies have indicated that the antibacterial and anticancer effects of the C. chinensis extract mainly come from the active polypeptides. Lysozyme is an effective immune effector in insect innate immunity and usually has excellent bactericidal effects. There are two kinds of lysozymes in insects, c-type and i-type, which play an important role in innate immunity and intestinal digestion. Studying lysozyme in C. chinensis will be helpful to further explore the evolutionary relationship and functional differences among lysozymes of various species and to determine whether they have biological activity and medicinal value. In this study, a lysozyme CcLys2 was identified from C. chinensis. CcLys2 contains 223 amino acid residues, and possesses a typical domain of the c-type lysozyme and a putative catalytic site formed by two conserved residues Glu32 and Asp50. Phylogenetic analysis showed that CcLys2 belongs to the H-branch of the c-type lysozyme. The analysis of spatiotemporal expression patterns indicated that CcLys2 was mainly expressed in the fat body of C. chinensis adults and was highly expressed in the second- and fifth-instar nymphs. In addition, CcLys2 was significantly up-regulated after injecting and feeding bacteria. In the bacterial inhibition assay, it was found that CcLys2 had antibacterial activity against Gram-positive bacteria at a low pH. These results indicate that CcLys2 has muramidase activity, involves in the innate immunity of C. chinensis, and is also closely related to the bacterial immune defense or digestive function of the intestine.

Sign in / Sign up

Export Citation Format

Share Document