scholarly journals Comparative analysis of MAPK and MKK gene families reveals differential evolutionary patterns in Brachypodium distachyon inbred lines

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11238
Author(s):  
Min Jiang ◽  
Peng Li ◽  
Wei Wang
Keyword(s):  
Differential Evolution ◽  
Stress Responses ◽  
Brachypodium Distachyon ◽  
Functional Divergence ◽  
Gene Families ◽  
Inbred Lines ◽  
Mitogen Activated Protein Kinase ◽  
Evolutionary Analysis ◽  
Biotic And Abiotic Stress ◽  
Evolutionary Patterns

Background Mitogen-activated protein kinase (MAPK) cascades are involved with signal transduction in almost every aspect of plant growth and development, as well as biotic and abiotic stress responses. The evolutionary analysis of MAPKs and MKKs in individual or entire plant species has been reported, but the evolutionary patterns in the diverse inbred lines of Brachypodium distachyon are still unclear. Results We conducted the systematical molecular evolutionary analysis of B. distachyon. A total of 799 MAPKs and 618 MKKs were identified from 53 B. distachyon inbred lines. Remarkably, only three inbred lines had 16 MPKs and most of those inbred lines lacked MPK7-2 members, whereas 12 MKKs existed in almost all B. distachyon inbred lines. Phylogenetic analysis indicated that MAPKs and MKKs were divided into four groups as previously reported, grouping them in the same branch as corresponding members. MPK21-2 was the exception and fell into two groups, which may be due to their exon-intron patterns, especially the untranslated regions (UTRs). We also found that differential evolution patterns of MKK10 paralogues from ancient tandem duplicates may have undergone functional divergence. Expression analyses suggested that MAPKs and MKKs likely played different roles in different genetic contexts within various tissues and with abiotic stresses. Conclusion Our study revealed that UTRs affected the structure and evolution of MPK21-2 genes and the differential evolution of MKK10 paralogues with ancient tandem duplication might have functional divergences. Our findings provide new insights into the functional evolution of genes in closely inbred lines.

scholarly journals Genome-Wide Identification and Analysis of MKK and MAPK Gene Families in Brassica Species and Response to Stress in Brassica napus

2021 ◽  
Vol 22 (2) ◽  
pp. 544
Author(s):  
Zhen Wang ◽  
Yuanyuan Wan ◽  
Xiaojing Meng ◽  
Xiaoli Zhang ◽  
Mengnan Yao ◽  
...  
Keyword(s):  
Stress Responses ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Brassica Species ◽  
Gene Families ◽  
Mitogen Activated Protein Kinase ◽  
Biotic And Abiotic Stress ◽  
Motif Analysis ◽  
Protein Motif ◽  
Mapk Gene

Mitogen-activated protein kinase (MAPK) cascades are common and conserved signal transduction pathways and play important roles in various biotic and abiotic stress responses and growth and developmental processes in plants. With the advancement of sequencing technology, more systematic genetic information is being explored. The work presented here focuses on two protein families in Brassica species: MAPK kinases (MKKs) and their phosphorylation substrates MAPKs. Forty-seven MKKs and ninety-two MAPKs were identified and extensively analyzed from two tetraploid (B. juncea and B. napus) and three diploid (B. nigra, B. oleracea, and B. rapa) Brassica species. Phylogenetic relationships clearly distinguished both MKK and MAPK families into four groups, labeled A–D, which were also supported by gene structure and conserved protein motif analysis. Furthermore, their spatial and temporal expression patterns and response to stresses (cold, drought, heat, and shading) were analyzed, indicating that BnaMKK and BnaMAPK transcript levels were generally modulated by growth, development, and stress signals. In addition, several protein interaction pairs between BnaMKKs and C group BnaMAPKs were detected by yeast two-hybrid assays, in which BnaMKK3 and BnaMKK9 showed strong interactions with BnaMAPK1/2/7, suggesting that interaction between BnaMKKs and C group BnaMAPKs play key roles in the crosstalk between growth and development processes and abiotic stresses. Taken together, our data provide a deeper foundation for the evolutionary and functional characterization of MKK and MAPK gene families in Brassica species, paving the way for unraveling the biological roles of these important signaling molecules in plants.

scholarly journals Genome-Wide Identification of CBL-CIPK Gene Family in Honeysuckle (Lonicera japonica Thunb.) and Their Regulated Expression Under Salt Stress

2021 ◽  
Vol 12 ◽  
Author(s):  
Luyao Huang ◽  
Zhuangzhuang Li ◽  
Qingxia Fu ◽  
Conglian Liang ◽  
Zhenhua Liu ◽  
...  
Keyword(s):  
Salt Stress ◽  
Protein Kinases ◽  
Stress Responses ◽  
Structure Prediction ◽  
Functional Divergence ◽  
Gene Families ◽  
Plant Responses ◽  
Interacting Protein ◽  
Protein Motifs ◽  
Insight Into

In plants, calcineurin B-like proteins (CBLs) are a unique group of Ca2+ sensors that decode Ca2+ signals by activating a family of plant-specific protein kinases known as CBL-interacting protein kinases (CIPKs). CBL-CIPK gene families and their interacting complexes are involved in regulating plant responses to various environmental stimuli. To gain insight into the functional divergence of CBL-CIPK genes in honeysuckle, a total of six LjCBL and 17 LjCIPK genes were identified. The phylogenetic analysis along with the gene structure analysis divided both CBL and CBL-interacting protein kinase genes into four subgroups and validated by the distribution of conserved protein motifs. The 3-D structure prediction of proteins shown that most LjCBLs shared the same Protein Data Bank hit 1uhnA and most LjCIPKs shared the 6c9Da. Analysis of cis-acting elements and gene ontology implied that both LjCBL and LjCIPK genes could be involved in hormone signal responsiveness and stress adaptation. Protein-protein interaction prediction suggested that LjCBL4 is hypothesized to interact with LjCIPK7/9/15/16 and SOS1/NHX1. Gene expression analysis in response to salinity stress revealed that LjCBL2/4, LjCIPK1/15/17 under all treatments gradually increased over time until peak expression at 72 h. These results demonstrated the conservation of salt overly sensitive pathway genes in honeysuckle and a model of Ca2+-LjCBL4/LjSOS3-LjCIPK16/LjSOS2 module-mediated salt stress signaling in honeysuckle is proposed. This study provides insight into the characteristics of the CBL-CIPK gene families involved in honeysuckle salt stress responses, which could serve as a foundation for gene transformation technology, to obtain highly salt-tolerant medicinal plants in the context of the global reduction of cultivated land.

scholarly journals Systematic Identification and Analysis of NAC Gene Family in Moso Bamboo (Phyllostachys edulis)

2020 ◽  
Author(s):  
Yameng Gao ◽  
Huanlong Liu ◽  
Lin Wu ◽  
Rui Xiong ◽  
Yanan Shi ◽  
...  
Keyword(s):  
Gene Family ◽  
Brachypodium Distachyon ◽  
Moso Bamboo ◽  
Evolutionary Analysis ◽  
Biotic And Abiotic Stress ◽  
Phyllostachys Edulis ◽  
Genome Data ◽  
Resistant Varieties ◽  
Nac Gene Family ◽  
Systematic Identification

Abstract Background: NAC (NAM/ATAF1/2/CUC2) gene family is a large plant-specific transcription factor family, which is implicated in many functions, such as morphogenesis, the thickness formation of secondary cell walls as well as biotic and abiotic stress and more. In moso bamboo ( Phyllostachys edulis ), 94 PeNACs have been identified and three members are predicted to relate to the secondary cell wall. However, there were few studies on moso bamboo NAC genes under stress.Results: In this study, we re-identified 165 PheNACs with the latest moso bamboo genome data and divided them into 12 subfamilies using NAM domains. Gene structure and motif distribution manifested the NAC gene family was fairly conserved. Evolutionary analysis showed that the segmental duplication played a significant role in the expansion of NAC genes and the relationship between moso bamboo and Brachypodium distachyon was closest than beween moso bamboo and other four species ( Arabidopsis thaliana, Oryza sativa , Sorghum bicolor and Zea mays ). Based on the promoter analysis of the 27 NAC members in A subfamily, quantitative real-time PCR exhibited these genes reacted differently under drought, high salt, abscisic acid and methyl jasmonate treatments. Finally, we selected out four potential stress-associated genes (PheNAC001, -056, -080 and -100) and found they all localized in the tobacco nucleus and had transcriptional activity in yeast.Conclusions: These preliminary results provide valuable information for mining potential resistance NAC genes and lay theoretical basis for breeding new stress-resistant varieties in moso bamboo.

scholarly journals Molecular Evolution, Genome-Wide Characterization and Codon Bias Analysis of the SBP-Box Family in Cucumis sativus

2019 ◽  
Author(s):  
Yue You ◽  
Yuanting Zheng ◽  
Jian Wang ◽  
Sujuan Li ◽  
Jianfeng Shao ◽  
...  
Keyword(s):  
Stress Responses ◽  
Codon Bias ◽  
Gene Families ◽  
Green Plant ◽  
Evolutionary Analysis ◽  
Bias Analysis ◽  
Regulatory Pathways ◽  
Genome Wide ◽  
Squamosa Promoter Binding Protein ◽  
Yield Quality

Abstract Background: SQUAMOSA promoter binding protein (SBP)-box genes encode a group of transcription factors which extensively play essential roles in plant development and stress responses. However, the SBP-box gene family has not been well characterized in cucumber (Cucumis sativas). Results: In present study, 15 putative SBP-box genes were identified distributing on 4 chromosomes of cucumber. Evolutionary analysis showed that the green plant SBP family originated from a common ancestor. Phylogenic analysis divided CuSBPs into 6 groups similar to those of Arabidopsis and rice. Intron-exon and motif structure within each group shared common features according to evolutionary study. Expression pattern analysis of transcriptional data about flowering and resistance to powdery mildew demonstrated conserved SBP-box genes function in vegetative-to-reproductive transition and potential roles in other regulatory pathways. Moreover, codon bias analysis explained the mutation and selection pressure exerted on genes. Conclusions: This study comprehensively characterized cucumber CuSBP gene families, which would provide a foundation to explore the functions of CuSBPs for improving yield, quality and stress tolerance of cucumber in the future.

Identification of a novel mitogen-activated protein kinase kinase gene (MKK2) in the oilseed rape Brassica campestris

Biologia ◽  
2014 ◽  
Vol 69 (11) ◽  
Author(s):  
Teng Zhang ◽  
Yuan Wang ◽  
Juan Wang ◽  
Xiao Xia ◽  
Ning Yang ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Stress Responses ◽  
Brassica Campestris ◽  
Plant Stress ◽  
Mitogen Activated Protein Kinase ◽  
Biotic And Abiotic Stress ◽  
Kinase Gene ◽  
Isolation And Characterization ◽  
Mapk Cascades ◽  
Mitogen Activated Protein

AbstractMitogen-activated protein kinase (MAPK) cascades participate in various processes, including plant growth and development as well as biotic and abiotic stress responses. MAPK kinases (MKKs), which link MPKs and MPKK kinases, are involved in MAPK cascades by mediating various plant stress responses. However, only a few MKKs from Brassica campestris (rape) have been functionally characterized. This study delivers the results from isolation and characterization of a novel gene, MKK2, from rape. Bioinformatics analysis revealed that the cDNA length of MKK2 is 1,344 bp with an open reading frame of 1,068 bp, which encodes a polypeptide containing 355 amino acids. The obtained MKK2 exhibited a predicted molecular mass of 39.3 kDa and an isoelectric point of 6.8. Quantitative real-time polymerase chain reaction analysis revealed that MKK2 expression can be induced by cold and salt. Western blot analysis revealed that MKK2 protein expression can be induced by cold, salt, and UV-B radiation. The MKK2 protein was localized in the nucleus. These results suggest that MKK2 is important for the regulation of cold- and salt-stress responses in plants.

scholarly journals Genome-Wide Identification, Evolution, and Expression Analysis of TPS and TPP Gene Families in Brachypodium distachyon

Plants ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 362 ◽  
Author(s):  
Song Wang ◽  
Kai Ouyang ◽  
Kai Wang
Keyword(s):  
Stress Responses ◽  
Brachypodium Distachyon ◽  
Interaction Network ◽  
Purifying Selection ◽  
Gene Interaction ◽  
Gene Families ◽  
Gene Interaction Network ◽  
Genome Wide ◽  
Duplication Events ◽  
Gene Structures

Trehalose biosynthesis enzyme homologues in plants contain two families, trehalose-6-phosphate synthases (TPSs) and trehalose-6-phosphate phosphatases (TPPs). Both families participate in trehalose synthesis and a variety of stress-resistance processes. Here, nine BdTPS and ten BdTPP genes were identified based on the Brachypodium distachyon genome, and all genes were classified into three classes. The Class I and Class II members differed substantially in gene structures, conserved motifs, and protein sequence identities, implying varied gene functions. Gene duplication analysis showed that one BdTPS gene pair and four BdTPP gene pairs are formed by duplication events. The value of Ka/Ks (non-synonymous/synonymous) was less than 1, suggesting purifying selection in these gene families. The cis-elements and gene interaction network prediction showed that many family members may be involved in stress responses. The quantitative real-time reverse transcription (qRT-PCR) results further supported that most BdTPSs responded to at least one stress or abscisic acid (ABA) treatment, whereas over half of BdTPPs were downregulated after stress treatment, implying that BdTPSs play a more important role in stress responses than BdTPPs. This work provides a foundation for the genome-wide identification of the B. distachyon TPS–TPP gene families and a frame for further studies of these gene families in abiotic stress responses.

scholarly journals Genome-Wide Identification and Characterization of the UBP Gene Family in Moso Bamboo (Phyllostachys edulis)

2019 ◽  
Vol 20 (17) ◽  
pp. 4309 ◽  
Author(s):  
Ruihua Wu ◽  
Yanrong Shi ◽  
Qian Zhang ◽  
Wenqing Zheng ◽  
Shaoliang Chen ◽  
...  
Keyword(s):  
Stress Responses ◽  
Brachypodium Distachyon ◽  
Divergence Time ◽  
Duplication Event ◽  
Moso Bamboo ◽  
Phyllostachys Edulis ◽  
Evolutionary Patterns ◽  
Genome Wide ◽  
Comparative Phylogenetic Analysis

The largest group of deubiquitinases—ubiquitin-specific proteases (UBPs)—perform extensive and significant roles in plants, including the regulation of development and stress responses. A comprehensive analysis of UBP genes has been performed in Arabidopsis thaliana, but no systematic study has been conducted in moso bamboo (Phyllostachys edulis). In this study, the genome-wide identification, classification, gene, protein, promoter region characterization, divergence time, and expression pattern analyses of the UBPs in moso bamboo were conducted. In total, 48 putative UBP genes were identified in moso bamboo, which were divided into 14 distinct subfamilies in accordance with a comparative phylogenetic analysis using 132 full-length protein sequences, including 48, 27, 25, and 32 sequences from moso bamboo, A. thaliana, rice (Oryza sativa), and purple false brome (Brachypodium distachyon), respectively. Analyses of the evolutionary patterns and divergence levels revealed that the PeUBP genes experienced a duplication event approximately 15 million years ago and that the divergence between PeUBP and OsUBP occurred approximately 27 million years ago. Additionally, several PeUBP members were significantly upregulated under abscisic acid, methyl jasmonate, and salicylic acid treatments, indicating their potential roles in abiotic stress responses in plants.

scholarly journals Conservation, Divergence, and Genome-Wide Distribution ofPALandPOX AGene Families in Plants

2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
H. C. Rawal ◽  
N. K. Singh ◽  
T. R. Sharma
Keyword(s):  
Gene Family ◽  
Populus Trichocarpa ◽  
Brachypodium Distachyon ◽  
Functional Divergence ◽  
Functional Characterization ◽  
Gene Families ◽  
Wide Distribution ◽  
Genome Wide ◽  
High Level ◽  
Diverse Groups

Genome-wide identification and phylogenetic and syntenic comparison were performed for the genes responsible for phenylalanine ammonia lyase (PAL) and peroxidase A (POX A) enzymes in nine plant species representing very diverse groups like legumes (Glycine maxandMedicago truncatula), fruits (Vitis vinifera), cereals (Sorghum bicolor,Zea mays, andOryza sativa), trees (Populus trichocarpa), and model dicot (Arabidopsis thaliana) and monocot (Brachypodium distachyon) species. A total of 87 and 1045 genes in PAL and POX A gene families, respectively, have been identified in these species. The phylogenetic and syntenic comparison along with motif distributions shows a high degree of conservation of PAL genes, suggesting that these genes may predate monocot/eudicot divergence. The POX A family genes, present in clusters at the subtelomeric regions of chromosomes, might be evolving and expanding with higher rate than the PAL gene family. Our analysis showed that during the expansion of POX A gene family, many groups and subgroups have evolved, resulting in a high level of functional divergence among monocots and dicots. These results will act as a first step toward the understanding of monocot/eudicot evolution and functional characterization of these gene families in the future.

scholarly journals Expansion and Functional Divergence of Inositol Polyphosphate 5-Phosphatases in Angiosperms

Genes ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 393 ◽  
Author(s):  
Zaibao Zhang ◽  
Yuting Li ◽  
Zhaoyi Luo ◽  
Shuwei Kong ◽  
Yilin Zhao ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Stress Responses ◽  
Functional Divergence ◽  
Purifying Selection ◽  
Ecological Niches ◽  
Evolutionary Analysis ◽  
Inositol Polyphosphate ◽  
Gene Copies ◽  
Group I

Inositol polyphosphate 5-phosphatase (5PTase), a key enzyme that hydrolyzes the 5′ position of the inositol ring, has essential functions in growth, development, and stress responses in plants, yeasts, and animals. However, the evolutionary history and patterns of 5PTases have not been examined systematically. Here, we report a comprehensive molecular evolutionary analysis of the 5PTase gene family and define four groups. These four groups are different from former classifications, which were based on in vitro substrate specificity. Most orthologous groups appear to be conserved as single or low-copy genes in all lineages in Groups II–IV, whereas 5PTase genes in Group I underwent several duplication events in angiosperm, resulting in multiple gene copies. Whole-genome duplication (WGD) was the main mechanism for 5PTase duplications in angiosperm. Plant 5PTases have more members than that of animals, and most plant 5PTase genes appear to have evolved under strong purifying selection. The paralogs have diverged in substrate specificity and expression pattern, showing evidence of selection pressure. Meanwhile, the increase in 5PTases and divergences in sequence, expression, and substrate might have contributed to the divergent functions of 5PTase genes, allowing the angiosperms to successfully adapt to a great number of ecological niches.

scholarly journals Update on the Roles of Rice MAPK Cascades

2021 ◽  
Vol 22 (4) ◽  
pp. 1679
Author(s):  
Jie Chen ◽  
Lihan Wang ◽  
Meng Yuan
Keyword(s):  
Signal Transduction ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Molecular Mechanisms ◽  
Developmental Regulation ◽  
Mitogen Activated Protein Kinase ◽  
Biotic And Abiotic Stress ◽  
Mapk Kinase ◽  
Mapk Cascades ◽  
Mitogen Activated Protein

The mitogen-activated protein kinase (MAPK) cascades have been validated playing critical roles in diverse aspects of plant biology, from growth and developmental regulation, biotic and abiotic stress responses, to phytohormone signal transduction or responses. A classical MAPK cascade consists of a MAPK kinase kinase (MAPKKK), a MAPK kinase (MAPKK), and a MAPK. From the 75 MAPKKKs, eight MAPKKs, and 15 MAPKs of rice, a number of them have been functionally deciphered. Here, we update recent advances in knowledge of the roles of rice MAPK cascades, including their components and complicated action modes, their diversified functions controlling rice growth and developmental responses, coordinating resistance to biotic and abiotic stress, and conducting phytohormone signal transduction. Moreover, we summarize several complete MAPK cascades that harbor OsMAPKKK-OsMAPKK-OsMAPK, their interaction with different upstream components and their phosphorylation of diverse downstream substrates to fulfill their multiple roles. Furthermore, we state a comparison of networks of rice MAPK cascades from signal transduction crosstalk to the precise selection of downstream substrates. Additionally, we discuss putative concerns for elucidating the underlying molecular mechanisms and molecular functions of rice MAPK cascades in the future.

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