scholarly journals Metal transporter encoding gene families in Fabaceae: III. The zinc-iron permease (ZIP) gene family

2020 ◽  
Vol 4 (1) ◽  
pp. First
Author(s):  
Cao Phi Bằng
Keyword(s):  
Plasma Membranes ◽  
Lotus Japonicus ◽  
Gene Families ◽  
Pigeon Pea ◽  
Gene Gain ◽  
Legume Species ◽  
Metal Transporter ◽  
Group I ◽  
Duplication Events ◽  
Zip Genes

In plants, Zinc and Iron are transported through the membrane by proteins belonging to Zinc-Iron permease (ZIP: ZRT/IRT-like Protein). In this work, the ZIP gene families were identified in the genome of five legume species. The results demonstrated that the ZIPs were belonged to a multigeneic family in each species including soybean (28 genes), Medicago truncalata (16 genes), chickpea (7 genes), pigeon pea (12 genes), and Lotus japonicus (15 genes). Each gene contained from one to twelve introns. ZIP proteins possessed a conserved histidine-rich motif. Most of these proteins contained eight putative transmembrane domains and were predicted to be localized in plasma membranes. The phylogeny analysis showed that the legume ZIPs were classified into four main groups, each of which includes many subgroups. The group I contained the ZIP members of five examined plants. Moreover, the phylogeny showed gene gain events (expansion) in group I and gene loss events in other groups. The gene expansion in group I is likely to have arisen mainly from recent duplication events of ZIP genes in the examined legume plants, after specialization. The expression analysis showed that all of ZIP genes were expressed in all of the examined tissues in L. japonicus. The expression level of ZIP members was not similar in different tissues of the plant. Some ZIP genes were predominantly expressed in certain tissues for most of the legume species investigated.

scholarly journals Metal transporter encoding gene families in Fabaceae: II. Cation/H+ exchanger (CAX) encoding genes

2017 ◽  
Vol 1 (T3) ◽  
pp. 27-36
Author(s):  
Bang Phi Cao ◽  
Anh Thi Van Le
Keyword(s):  
Gene Duplication ◽  
Transmembrane Helix ◽  
Gene Families ◽  
Full Length ◽  
Legume Species ◽  
Base Pairs ◽  
Metal Transporter ◽  
Phylogeny Analysis ◽  
Multigenic Family ◽  
Encoding Genes

The plant CAtion/H+ eXchangers (CAX) proteins belong to Ca2+/cation antiporter (CaCA) superfamily. By using in silico methods, the CAX encoding genes in the genome of six legume species have been identified in this work. In examined legume genomes, the CAX genes belong to a small multigenic family. The number of the CAX genes in these legume species is 17 (soybean), 6 (common bean and C. cajan), 5 (M. truncatula and C. arietinum) and 3 genes (L. japonicus), respectively. The legume CAX genes vary in genomic full-length ranging from 1,213 to 11,561 base pairs. All of the genes exhibit introns (from 4 to 11 introns). Their deduced full-length protein sequences range from 248 to 718 amino acids. Theoretical pI values of most (39/42) of legume CAX proteins were less than 7. The secondary structure modelling of protein exhibit transmembrane helix region (from 3 to 11 regions). Half of all (23/42) included 11 transmembrane helix regions. Based on phylogeny analysis, all of the legume CAX were divided into two groups, A and B, each consisting of two subgroups. The phylogeny suggested an ancient gene duplication in the genome of legumes ancestry. The recent gene duplication even was only detected in the soybean genome after the speciation. The expression analysis showed that all of 3 L. japonicus CAX genes expressed in all examined tissues. However, the expression of C. cajan CAX genes was not detected. For each of 4 remaining legumes, the CAX genes were differed in their expression level depending on studied tissues. The tissue-specific expressions of some CAX genes were observed in 5 out of the 6 legume species, except C. cajan.

scholarly journals Genomic Organization and Evolutionary Insights on GRP and NCR Genes, Two Large Nodule-Specific Gene Families in Medicago truncatula

2007 ◽  
Vol 20 (9) ◽  
pp. 1138-1148 ◽  
Author(s):  
Benoit Alunni ◽  
Zoltan Kevei ◽  
Miguel Redondo-Nieto ◽  
Adam Kondorosi ◽  
Peter Mergaert ◽  
...  
Keyword(s):  
Medicago Truncatula ◽  
Evolutionary Dynamics ◽  
Genomic Organization ◽  
Phylogenetic Analyses ◽  
Lotus Japonicus ◽  
Gene Families ◽  
Specific Gene ◽  
Specific Expression ◽  
Duplication Events ◽  
Protein Alignments

Deciphering the mechanisms leading to symbiotic nitrogen-fixing root nodule organogenesis in legumes resulted in the identification of numerous nodule-specific genes and gene families. Among them, NCR and GRP genes encode short secreted peptides with potential antimicrobial activity. These genes appear to form large multigenic families in Medicago truncatula and other closely related legume species, whereas no similar genes were found in databases of Lotus japonicus and Glycine max. We analyzed the genomic organization of these genes as well as their evolutionary dynamics in the M. truncatula genome. A total of 108 NCR and 23 GRP genes have been mapped that were often clustered in the genome. These included 29 new NCR and 17 new GRP genes. Reverse transcription-polymerase chain reaction analyses of the novel genes confirmed their exclusive nodule-specific expression similar to the previously identified members. Protein alignments and phylogenetic analyses revealed traces of several duplication events in the history of GRP and NCR genes. Moreover, microsyntenic evidences between M. truncatula and L. japonicus validated the hypothesis that these genes are specific for the inverted repeat–lacking clade of hologalegoid legumes, which allowed dating the appearance of these two gene families during the evolution of legume plants.

scholarly journals Plasmids Related to the Symbiotic Nitrogen Fixation Are Not Only Cooperated Functionally but Also May Have Evolved over a Time Span in Family Rhizobiaceae

2020 ◽  
Vol 12 (11) ◽  
pp. 2002-2014
Author(s):  
Ling-Ling Yang ◽  
Zhao Jiang ◽  
Yan Li ◽  
En-Tao Wang ◽  
Xiao-Yang Zhi
Keyword(s):  
Nitrogen Fixation ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Symbiotic Nitrogen Fixation ◽  
Gene Families ◽  
Time Span ◽  
Soil Conditions ◽  
Gene Gain ◽  
Nitrogen Fixing ◽  
Pan Genome

Abstract Rhizobia are soil bacteria capable of forming symbiotic nitrogen-fixing nodules associated with leguminous plants. In fast-growing legume-nodulating rhizobia, such as the species in the family Rhizobiaceae, the symbiotic plasmid is the main genetic basis for nitrogen-fixing symbiosis, and is susceptible to horizontal gene transfer. To further understand the symbioses evolution in Rhizobiaceae, we analyzed the pan-genome of this family based on 92 genomes of type/reference strains and reconstructed its phylogeny using a phylogenomics approach. Intriguingly, although the genetic expansion that occurred in chromosomal regions was the main reason for the high proportion of low-frequency flexible gene families in the pan-genome, gene gain events associated with accessory plasmids introduced more genes into the genomes of nitrogen-fixing species. For symbiotic plasmids, although horizontal gene transfer frequently occurred, transfer may be impeded by, such as, the host’s physical isolation and soil conditions, even among phylogenetically close species. During coevolution with leguminous hosts, the plasmid system, including accessory and symbiotic plasmids, may have evolved over a time span, and provided rhizobial species with the ability to adapt to various environmental conditions and helped them achieve nitrogen fixation. These findings provide new insights into the phylogeny of Rhizobiaceae and advance our understanding of the evolution of symbiotic nitrogen fixation.

Structural diversity of band 4.1 superfamily members

1994 ◽  
Vol 107 (7) ◽  
pp. 1921-1928 ◽  
Author(s):  
K. Takeuchi ◽  
A. Kawashima ◽  
A. Nagafuchi ◽  
S. Tsukita
Keyword(s):  
Plasma Membrane ◽  
Tyrosine Kinases ◽  
Plasma Membranes ◽  
Structural Diversity ◽  
Gene Families ◽  
Cdna Clones ◽  
New Members ◽  
F9 Cells ◽  
Novel Proteins ◽  
Cellular Events

Several proteins contain the domain homologous to the N-terminal half of band 4.1 protein, indicating the existence of a superfamily. The members of this ‘band 4.1’ superfamily are thought to play crucial roles in the regulation of cytoskeleton-plasma membrane interaction just beneath plasma membranes. We examined the structural diversity of this superfamily by means of the polymerase chain reaction using synthesized mixed primers. We thus identified many members of the band 4.1 superfamily that were expressed in mouse teratocarcinoma F9 cells and mouse brain tissue. In total, 15 cDNA clones were obtained; 8 were identical to the corresponding parts of cDNAs for the known members, while 7 appeared to encode novel proteins (NBL1-7: novel band 4.1-like proteins). Sequence analyses of these clones revealed that the band 4.1 superfamily can be subdivided into 5 gene families; band 4.1 protein, ERM (ezrin/radixin/moesin/merlin/NBL6/NBL7+ ++), talin, PTPH1 (PTPH1/PTPMEG/NBL1-3), and NBL4 (NBL4/NBL5) families. The NBL4 family was first identified here, and the full-length cDNA encoding NBL4 was cloned. The deduced amino acid sequence revealed a myristoylation site, as well as phosphorylation sites for A-kinase and tyrosine kinases in its N-terminal half, suggesting its involvement in the phosphorylation-dependent regulation of cellular events just beneath the plasma membrane. In this study, we describe the initial characterization of these new members and discuss the evolution of the band 4.1 superfamily.

scholarly journals Global Survey and Expressions of the Phosphate Transporter Gene Families in Brassica napus and Their Roles in Phosphorus Response

2020 ◽  
Vol 21 (5) ◽  
pp. 1752 ◽  
Author(s):  
Jin Yang ◽  
Jie Zhou ◽  
Hong-Jun Zhou ◽  
Mang-Mang Wang ◽  
Ming-Ming Liu ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Expression Profiles ◽  
Phylogenetic Analyses ◽  
Functional Divergence ◽  
Gene Families ◽  
Small Scale ◽  
Transporter Gene ◽  
Promoter Regions ◽  
Network Analyses ◽  
Group I

Phosphate (Pi) transporters play critical roles in Pi acquisition and homeostasis. However, currently little is known about these genes in oil crops. In this study, we aimed to characterize the five Pi transporter gene families (PHT1-5) in allotetraploid Brassica napus. We identified and characterized 81 putative PHT genes in B. napus (BnaPHTs), including 45 genes in PHT1 family (BnaPHT1s), four BnaPHT2s, 10 BnaPHT3s, 13 BnaPHT4s and nine BnaPHT5s. Phylogenetic analyses showed that the largest PHT1 family could be divided into two groups (Group I and II), while PHT4 may be classified into five, Groups I-V. Gene structure analysis revealed that the exon-intron pattern was conservative within the same family or group. The sequence characteristics of these five families were quite different, which may contribute to their functional divergence. Transcription factor (TF) binding network analyses identified many potential TF binding sites in the promoter regions of candidates, implying their possible regulating patterns. Collinearity analysis demonstrated that most BnaPHTs were derived from an allopolyploidization event (~40.7%) between Brassica rapa and Brassica oleracea ancestors, and small-scale segmental duplication events (~39.5%) in the descendant. RNA-Seq analyses proved that many BnaPHTs were preferentially expressed in leaf and flower tissues. The expression profiles of most colinearity-pairs in B. napus are highly correlated, implying functional redundancy, while a few pairs may have undergone neo-functionalization or sub-functionalization during evolution. The expression levels of many BnaPHTs tend to be up-regulated by different hormones inductions, especially for IAA, ABA and 6-BA treatments. qRT-PCR assay demonstrated that six BnaPHT1s (BnaPHT1.11, BnaPHT1.14, BnaPHT1.20, BnaPHT1.35, BnaPHT1.41, BnaPHT1.44) were significantly up-regulated under low- and/or rich- Pi conditions in B. napus roots. This work analyzes the evolution and expression of the PHT family in Brassica napus, which will help further research on their role in Pi transport.

scholarly journals Ecological correlates of gene family size: the draft genome of the redheaded pine sawfly Neodiprion lecontei

2021 ◽  
Author(s):  
Kim Vertacnik ◽  
Danielle Herrig ◽  
R Keating Godfrey ◽  
Tom Hill ◽  
Scott Geib ◽  
...  
Keyword(s):  
Gene Family ◽  
Family Size ◽  
Draft Genome ◽  
Gene Families ◽  
Gene Family Evolution ◽  
Gene Gain ◽  
Ecological Specialization ◽  
Dietary Specialization ◽  
Pine Sawfly ◽  
Neodiprion Lecontei

A central goal in evolutionary biology is to determine the predictability of adaptive genetic changes. Despite many documented cases of convergent evolution at individual loci, little is known about the repeatability of gene family expansions and contractions. To address this void, we examined gene family evolution in the redheaded pine sawfly Neodiprion lecontei, a non-eusocial hymenopteran and exemplar of a pine-specialized lineage evolved from angiosperm-feeding ancestors. After assembling and annotating a draft genome, we manually annotated multiple gene families with chemosensory, detoxification, or immunity functions and characterized their genomic distributions and evolutionary history. Our results suggest that expansions of bitter gustatory receptor (GR), clan 3 cytochrome P450 (CYP3), and antimicrobial peptide (AMP) subfamilies may have contributed to pine adaptation. By contrast, there was no evidence of recent gene family contraction via pseudogenization. Next, we compared the number of genes in these same families across insect taxa that vary in diet, dietary specialization, and social behavior. In Hymenoptera, herbivory was associated with large GR and small olfactory receptor (OR) families, eusociality was associated with large OR and small AMP families, and--unlike investigations among more closely related taxa--ecological specialization was not related to gene family size. Overall, our results suggest that gene families that mediate ecological interactions may expand and contract predictably in response to particular selection pressures, however, the ecological drivers and temporal pace of gene gain and loss likely varies considerably across gene families.

Fructosyltransferase and invertase genes evolved by gene duplication and rearrangements: rice, perennial ryegrass, and wheat gene families

Genome ◽  
2006 ◽  
Vol 49 (9) ◽  
pp. 1081-1091 ◽  
Author(s):  
Michael G. Francki ◽  
Esther Walker ◽  
John W. Forster ◽  
German Spangenberg ◽  
Rudi Appels
Keyword(s):  
Perennial Ryegrass ◽  
Abiotic Stress Tolerance ◽  
Gene Families ◽  
Amino Acid Similarity ◽  
Gene Variation ◽  
Wheat Gene ◽  
Multiple Copies ◽  
Duplication Events ◽  
Invertase Gene ◽  
Gene Orthologs

The invertase enzyme family is responsible for carbohydrate metabolism in rice, perennial ryegrass, and wheat. Fructan molecules accumulate in cell vacuoles of perennial ryegrass and wheat and are associated with abiotic stress tolerance. High levels of amino acid similarity between the fructosyltransferases responsible for fructan accumulation indicates that they may have evolved from invertase-like ancestral genes. In this study, we have applied comparative genomics to determine the mechanisms that lead to the evolution of fructosytransferase and invertase genes in rice, perennial ryegrass, and wheat. Duplications and rearrangements have been inferred to generate variant forms of the rice invertases since divergence from a common grass progenitor. The occurrence of multiple copies of fructosyltransferase genes indicated that duplication events continued during evolution of the wheat and perennial ryegrass lineages. Further gene rearrangements were evident in perennial ryegrass genes, albeit at a reduced level compared with the rice invertases. Gene orthologs were largely static after duplication during evolution of the wheat lineage. This study details evolutionary events that contribute to fructosyltransferase and invertase gene variation in grasses.

scholarly journals Evolutionary Plasticity in Detoxification Gene Modules: The Preservation and Loss of the Pregnane X Receptor in Chondrichthyes Lineages

2019 ◽  
Vol 20 (9) ◽  
pp. 2331 ◽  
Author(s):  
Elza S. S. Fonseca ◽  
Raquel Ruivo ◽  
André M. Machado ◽  
Francisca Conrado ◽  
Boon-Hui Tay ◽  
...  
Keyword(s):  
Functional Characterization ◽  
Constitutive Androstane Receptor ◽  
Pregnane X Receptor ◽  
Gene Families ◽  
Critical Question ◽  
Group I ◽  
Activation Profile ◽  
Gene Duplication And Loss ◽  
Molecular Landscape ◽  
Gene Orthologs

To appraise how evolutionary processes, such as gene duplication and loss, influence an organism’s xenobiotic sensitivity is a critical question in toxicology. Of particular importance are gene families involved in the mediation of detoxification responses, such as members of the nuclear receptor subfamily 1 group I (NR1I), the pregnane X receptor (PXR), and the constitutive androstane receptor (CAR). While documented in multiple vertebrate genomes, PXR and CAR display an intriguing gene distribution. PXR is absent in birds and reptiles, while CAR shows a tetrapod-specific occurrence. More elusive is the presence of PXR and CAR gene orthologs in early branching and ecologically-important Chondrichthyes (chimaeras, sharks and rays). Therefore, we investigated various genome projects and use them to provide the first identification and functional characterization of a Chondrichthyan PXR from the chimaera elephant shark (Callorhinchus milii, Holocephali). Additionally, we substantiate the targeted PXR gene loss in Elasmobranchii (sharks and rays). Compared to other vertebrate groups, the chimaera PXR ortholog displays a diverse expression pattern (skin and gills) and a unique activation profile by classical xenobiotic ligands. Our findings provide insights into the molecular landscape of detoxification mechanisms and suggest lineage-specific adaptations in response to xenobiotics in gnathostome evolution.

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