Genes encoding the α-carboxyltransferase subunit of acetyl-CoA carboxylase from Brassica napus and parental species: cloning, expression patterns, and evolution

Genome ◽  
2010 ◽  
Vol 53 (5) ◽  
pp. 360-370 ◽  
Author(s):  
Zhi-Guo Li ◽  
Wei-Bo Yin ◽  
Huan Guo ◽  
Li-Ying Song ◽  
Yu-Hong Chen ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Fatty Acid Biosynthesis ◽  
Parental Species ◽  
Expression Patterns ◽  
Brassica Species ◽  
Orthologous Gene ◽  
Glucuronidase Activity ◽  
Genes Encoding ◽  
Group 2 ◽  
Group 1

Heteromeric acetyl coenzyme A carboxylase (ACCase), a rate-limiting enzyme in fatty acid biosynthesis in dicots, is a multi-enzyme complex consisting of biotin carboxylase, biotin carboxyl carrier protein, and carboxyltransferase (α-CT and β-CT). In the present study, four genes encoding α-CT were cloned from Brassica napus , and two were cloned from each of the two parental species, B. rapa and B. oleracea . Comparative and cluster analyses indicated that these genes were divided into two major groups. The major divergence between group-1 and group-2 occurred in the second intron. Group-2 α-CT genes represented the ancestral form in the genus Brassica. The divergence of group-1 and group-2 genes occurred in their common ancestor 12.96–17.78 million years ago (MYA), soon after the divergence of Arabidopsis thaliana and Brassica (15–20 MYA). This time of divergence is identical to that reported for the paralogous subgenomes of diploid Brassica species (13–17 MYA). Real-time reverse transcription PCR revealed that the expression patterns of the two groups of genes were similar in different organs, except in leaves. To better understand the regulation and evolution of α-CT genes, promoter regions from two sets of orthologous gene copies from B. napus, B. rapa, and B. oleracea were cloned and compared. The function of the promoter of gene Bnα-CT-1-1 in group-1 and gene Bnα-CT-2-1 in group-2 was examined by assaying β-glucuronidase activity in transgenic A. thaliana. Our results will be helpful in elucidating the evolution and regulation of ACCase in oilseed rape.

Genes encoding the biotin carboxylase subunit of acetyl-CoA carboxylase from Brassica napus and parental species: cloning, expression patterns, and evolution

Genome ◽  
2011 ◽  
Vol 54 (3) ◽  
pp. 202-211 ◽  
Author(s):  
Zhi-Guo Li ◽  
Wei-Bo Yin ◽  
Li-Ying Song ◽  
Yu-Hong Chen ◽  
Rong-Zhan Guan ◽  
...  
Keyword(s):  
Amino Acid ◽  
Brassica Napus ◽  
Parental Species ◽  
Expression Patterns ◽  
Carrier Protein ◽  
Acetyl Coa Carboxylase ◽  
Transit Peptides ◽  
Genes Encoding ◽  
Group 2 ◽  
Group 1

Comparative genomics is a useful tool to investigate gene and genome evolution. Biotin carboxylase (BC), an important subunit of heteromeric acetyl-CoA carboxylase (ACCase) that is a rate-limiting enzyme in fatty acid biosynthesis in dicots, catalyzes ATP, biotin carboxyl carrier protein, and CO2 to form carboxybiotin carboxyl carrier protein. In this study, we cloned four genes encoding BC from Brassica napus L. (namely BnaC.BC.a, BnaC.BC.b, BnaA.BC.a, and BnaA.BC.b), and two were cloned from each of the two parental species Brassica rapa L. (BraA.BC.a and BraA.BC.b) and Brassica oleracea L. (BolC.BC.a and BolC.BC.b). Sequence analyses revealed that in B. napus the genes BnaC.BC.a and BnaC.BC.b were from the C genome of B. oleracea, whereas BnaA.BC.a and BnaA.BC.b were from the A genome of B. rapa. Comparative and cluster analysis indicated that these genes were divided into two major groups, BnaC.BC.a, BnaA.BC.a, BraA.BC.a, and BolC.BC.a in group-1 and BnaC.BC.b, BnaA.BC.b, BraA.BC.b, and BolC.BC.b in group-2. The divergence of group-1 and group-2 genes occurred in their common ancestor 13–17 million years ago (MYA), soon after the divergence of Arabidopsis and Brassica (15–20 MYA). This time of divergence is identical to the previously reported triplicated time of paralogous subgenomes of diploid Brassica species and the divergence date of group-1 and group-2 genes of α-carboxyltransferase, another subunit of heteromeric ACCase, in Brassica. Reverse transcription PCR revealed that the expression level of group-1 and group-2 genes varied in different organs, and the expression patterns of the two groups of genes were similar in different organs, except in flower. However, two paralogs of group-2 BC genes from B. napus could express differently in mature plants tested by generating BnaA.BC.b and BnaC.BC.b promoter–β-glucuronidase (GUS) fusions. The amino acid sequences of proteins encoded by these genes were highly conserved, except the sequence encoding predicted plastid transit peptides. The plastid transit peptides on the BC precursors of Brassica (71–72 amino acid residues) were predicted based on AtBC protein, compared, and confirmed by fusion with green fluorescent protein. Our results will be helpful in elucidating the evolution and the regulation of ACCase in the genus Brassica.

scholarly journals Two Auxinic Herbicides Affect Brassica napus Plant Hormone Levels and Induce Molecular Changes in Transcription

Biomolecules ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1153
Author(s):  
Jutta Ludwig-Müller ◽  
Roman Rattunde ◽  
Sabine Rößler ◽  
Katja Liedel ◽  
Freia Benade ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Expression Patterns ◽  
Growth Conditions ◽  
Growth Stages ◽  
Auxin Response ◽  
Time Points ◽  
Genes Encoding ◽  
Different Temperatures ◽  
Indigenous Plant ◽  
Over Time

With the introduction of the new auxinic herbicide halauxifen-methyl into the oilseed rape (Brassica napus) market, there is a need to understand how this new molecule interacts with indigenous plant hormones (e.g., IAA) in terms of crop response. The aim of this study was to investigate the molecular background by using different growth conditions under which three different auxinic herbicides were administered. These were halauxifen-methyl (Hal), alone and together with aminopyralid (AP) as well as picloram (Pic). Three different hormone classes were determined, free and conjugated indole-3-acetic acid (IAA), aminocyclopropane carboxylic acid (ACC) as a precursor for ethylene, and abscisic acid (ABA) at two different temperatures and growth stages as well as over time (2–168 h after treatment). At 15 °C growth temperature, the effect was more pronounced than at 9 °C, and generally, the younger leaves independent of the developmental stage showed a larger effect on the alterations of hormones. IAA and ACC showed reproducible alterations after auxinic herbicide treatments over time, while ABA did not. Finally, a transcriptome analysis after treatment with two auxinic herbicides, Hal and Pic, showed different expression patterns. Hal treatment leads to the upregulation of auxin and hormone responses at 48 h and 96 h. Pic treatment induced the hormone/auxin response already after 2 h, and this continued for the other time points. The more detailed analysis of the auxin response in the datasets indicate a role for GH3 genes and genes encoding auxin efflux proteins. The upregulation of the GH3 genes correlates with the increase in conjugated IAA at the same time points and treatments. Also, genes for were found that confirm the upregulation of the ethylene pathway.

scholarly journals Mamu-B*17+Rhesus Macaques Vaccinated withenv,vif, andnefManifest Early Control of SIVmac239 Replication

2018 ◽  
Vol 92 (16) ◽  
Author(s):  
Mauricio A. Martins ◽  
Damien C. Tully ◽  
Núria Pedreño-Lopez ◽  
Benjamin von Bredow ◽  
Matthias G. Pauthner ◽  
...  
Keyword(s):  
T Cells ◽  
Rhesus Macaques ◽  
Chronic Phase ◽  
Virologic Suppression ◽  
Mhc I ◽  
Immunodeficiency Virus ◽  
Genes Encoding ◽  
Siv Infection ◽  
Group 2 ◽  
Group 1

ABSTRACTCertain major histocompatibility complex class I (MHC-I) alleles are associated with spontaneous control of viral replication in human immunodeficiency virus (HIV)-infected people and simian immunodeficiency virus (SIV)-infected rhesus macaques (RMs). These cases of “elite” control of HIV/SIV replication are often immune-mediated, thereby providing a framework for studying anti-lentiviral immunity. In this study, we examined how vaccination impacts SIV replication in RMs expressing the MHC-I alleleMamu-B*17. Approximately 21% ofMamu-B*17+and 50% ofMamu-B*08+RMs control chronic-phase viremia after SIVmac239 infection. Because CD8+T cells targeting Mamu-B*08-restricted SIV epitopes have been implicated in virologic suppression inMamu-B*08+RMs, we investigated whether this might also be true forMamu-B*17+RMs. Two groups ofMamu-B*17+RMs were vaccinated with genes encoding Mamu-B*17-restricted epitopes in Vif and Nef. These genes were delivered by themselves (group 1) or together withenv(group 2). Group 3 included MHC-I-matched RMs and served as the control group. Surprisingly, the group 1 vaccine regimen had little effect on viral replication compared to group 3, suggesting that unlikeMamu-B*08+RMs, preexisting SIV-specific CD8+T cells alone do not facilitate long-term virologic suppression inMamu-B*17+RMs. Remarkably, however, 5/8 group 2 vaccinees controlled viremia to <15 viral RNA copies/ml soon after infection. No serological neutralizing activity against SIVmac239 was detected in group 2, although vaccine-elicited gp140-binding antibodies correlated inversely with nadir viral loads. Collectively, these data shed new light on the unique mechanism of elite control inMamu-B*17+RMs and implicate vaccine-induced, nonneutralizing anti-Env antibodies in the containment of immunodeficiency virus infection.IMPORTANCEA better understanding of the immune correlates of protection against HIV might facilitate the development of a prophylactic vaccine. Therefore, we investigated simian immunodeficiency virus (SIV) infection outcomes in rhesus macaques expressing the major histocompatibility complex class I alleleMamu-B*17. Approximately 21% ofMamu-B*17+macaques spontaneously controlled chronic phase viremia after SIV infection, an effect that may involve CD8+T cells targeting Mamu-B*17-restricted SIV epitopes. We vaccinatedMamu-B*17+macaques with genes encoding immunodominant epitopes in Vif and Nef alone (group 1) or together withenv(group 2). Although neither vaccine regimen prevented SIV infection, 5/8 group 2 vaccinees controlled viremia to below detection limits shortly after infection. This outcome, which was not observed in group 1, was associated with vaccine-induced, nonneutralizing Env-binding antibodies. Together, these findings suggest a limited contribution of Vif- and Nef-specific CD8+T cells for virologic control inMamu-B*17+macaques and implicate anti-Env antibodies in containment of SIV infection.

Global genetic diversity in oilseed Brassica rapa

2013 ◽  
Vol 64 (10) ◽  
pp. 993 ◽  
Author(s):  
Annisa ◽  
S. Chen ◽  
W. A. Cowling
Keyword(s):  
Brassica Rapa ◽  
Genetic Variance ◽  
Allelic Diversity ◽  
Unknown Origin ◽  
Brassica Species ◽  
Pollination Control ◽  
Group 3 ◽  
Group 2 ◽  
Simple Sequence ◽  
Group 1

Three major simple sequence repeat (SSR) groups were identified in a global collection of 164 oilseed Brassica rapa based on allelic diversity at loci: SSR group 1 (south Asia, predominantly from India, Pakistan, and Nepal); SSR group 2 (predominantly southern and eastern Europe with mostly winter and semi-winter types); and SSR group 3 (northern Europe, mostly from Germany, and many of unknown origin). Nine outliers from several regions were placed in a fourth SSR group, which had the highest allelic diversity per accession of all SSR groups. Analysis of molecular variance of SSR data supported four groups but indicated that genetic variance within populations was high (84%) compared with variance between populations. Flowering habit was classified as winter, spring or semi-winter type, and pollination control as self-incompatible or self-compatible. These phenotypes were distributed across each of the three SSR groups and outliers, although most SSR group 1 accessions were self-compatible spring types, and winter types were mainly from SSR groups 2 and 3. Two SSR sub-groups were present among Indian accessions, both of which contained brown-seeded types, but only one sub-group contained yellow-seeded types (most likely yellow sarson). Eleven B. rapa accessions were misclassified in genebanks as oilseed types but were re-classified as leafy or root vegetable types, and 12 accessions were misclassified as B. rapa and were shown to be allotetraploid or other Brassica species.

scholarly journals Three Homologous Genes Encoding sn-Glycerol-3-Phosphate Acyltransferase 4 Exhibit Different Expression Patterns and Functional Divergence in Brassica napus

2010 ◽  
Vol 155 (2) ◽  
pp. 851-865 ◽  
Author(s):  
Xue Chen ◽  
Martin Truksa ◽  
Crystal L. Snyder ◽  
Aliaa El-Mezawy ◽  
Saleh Shah ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Homologous Genes ◽  
Genes Encoding

scholarly journals Genome-Wide Analysis of the YABBY Transcription Factor Family in Rapeseed (Brassica napus L.)

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 981
Author(s):  
Jichun Xia ◽  
Dong Wang ◽  
Yuzhou Peng ◽  
Wenning Wang ◽  
Qianqian Wang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Brassica Species ◽  
Pcr Analysis ◽  
Sequencing Data ◽  
Functional Identification ◽  
Brassica Napus L ◽  
Intron Structure ◽  
Duplication Events

The YABBY family of plant-specific transcription factors play important regulatory roles during the development of leaves and floral organs, but their functions in Brassica species are incompletely understood. Here, we identified 79 YABBY genes from Arabidopsis thaliana and five Brassica species (B. rapa, B. nigra, B. oleracea, B. juncea, and B. napus). A phylogenetic analysis of YABBY proteins separated them into five clusters (YAB1–YAB5) with representatives from all five Brassica species, suggesting a high degree of conservation and similar functions within each subfamily. We determined the gene structure, chromosomal location, and expression patterns of the 21 BnaYAB genes identified, revealing extensive duplication events and gene loss following polyploidization. Changes in exon–intron structure during evolution may have driven differentiation in expression patterns and functions, combined with purifying selection, as evidenced by Ka/Ks values below 1. Based on transcriptome sequencing data, we selected nine genes with high expression at the flowering stage. qRT-PCR analysis further indicated that most BnaYAB family members are tissue-specific and exhibit different expression patterns in various tissues and organs of B. napus. This preliminary study of the characteristics of the YABBY gene family in the Brassica napus genome provides theoretical support and reference for the later functional identification of the family genes.

scholarly journals Stigmasterol blocks cartilage degradation in rabbit model of osteoarthritis.

2012 ◽  
Vol 59 (4) ◽  
Author(s):  
Wei-Ping Chen ◽  
Chong Yu ◽  
Peng-Fei Hu ◽  
Jia-Peng Bao ◽  
Jing-Li Tang ◽  
...  
Keyword(s):  
Cruciate Ligament ◽  
Rabbit Model ◽  
Cartilage Degradation ◽  
Tissue Inhibitors Of Metalloproteinase ◽  
Expression Of Genes ◽  
Genes Encoding ◽  
Group 2 ◽  
Group 1

Stigmasterol has been shown exhibit anti-osteoarthritic properties in vitro studies. However, the in vivo effects of stigmasterol on cartilage are still unclear. This study investigated the anti-osteoarthritic properties of stigmasterol on cartilage degradation in a rabbit model of osteoarthritis (OA). Twenty rabbits underwent bilateral anterior cruciate ligament transection (ACLT) to induce OA. Five rabbits were used as normal control. Two weeks after operation, the rabbits were randomly divided into two groups. Each group of 10 rabbits received intra-articular injection with 0.3 ml of stigmasterol in left knees and vehicle in right knees, once weekly. Group 1 was killed 6 weeks after ACLT and 2 were sacrificed 9 weeks after ACLT. The knee joints were assessed by gross morphology, histology and gene expression analysis. We found that expression of genes encoding matrix metalloproteinases (MMPs) was significantly higher while tissue inhibitors of metalloproteinase (TIMP)-1 was significantly lower in the both joints of the two OA groups compared to normal controls. Stigmasterol reduced the cartilage degradation as assessed by histological analysis and markedly suppressed MMPs expression both in group 1 and group 2. Our results suggest that stigmasterol may be considered as a possible therapeutical agent in the treatment of OA.

scholarly journals Comprehensive Analysis of the SUV Gene Family in Allopolyploid Brassica napus and Its Diploid Ancestors

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1848
Author(s):  
Meimei Hu ◽  
Mengdi Li ◽  
Jianbo Wang
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Expression Patterns ◽  
Protein Structures ◽  
Evolutionary Process ◽  
Orthologous Gene ◽  
Evolutionary Relationships ◽  
Protein Motifs ◽  
Gene Pairs ◽  
Gene Structures

SUV (the Suppressor of variegation [Su(var)] homologs and related) gene family is a subgroup of the SET gene family. According to the SRA domain and WIYLD domain distributions, it can be divided into two categories, namely SUVH (the Suppressor of variegation [Su(var)] homologs) and SUVR (the Suppressor of variegation [Su(var)] related). In this study, 139 SUV genes were identified in allopolyploid Brassica napus and its diploid ancestors, and their evolutionary relationships, protein properties, gene structures, motif distributions, transposable elements, cis-acting elements and gene expression patterns were analyzed. Our results showed that the SUV gene family of B. napus was amplified during allopolyploidization, in which the segmental duplication and TRD played critical roles. After the separation of Brassica and Arabidopsis lineages, orthologous gene analysis showed that many SUV genes were lost during the evolutionary process in B. rapa, B. oleracea and B. napus. The analysis of the gene and protein structures and expression patterns of 30 orthologous gene pairs which may have evolutionary relationships showed that most of them were conserved in gene structures and protein motifs, but only four gene pairs had the same expression patterns.

scholarly journals Genome-Wide Identification of Flowering-Time Genes in Brassica Species and Reveals a Correlation between Selective Pressure and Expression Patterns of Vernalization-Pathway Genes in Brassica napus

2018 ◽  
Vol 19 (11) ◽  
pp. 3632 ◽  
Author(s):  
Haojie Li ◽  
Yonghai Fan ◽  
Jingyin Yu ◽  
Liang Chai ◽  
Jingfang Zhang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Flowering Time ◽  
Expression Patterns ◽  
Brassica Species ◽  
Synonymous Substitution ◽  
Selection Pressures ◽  
Evolutionary Selection ◽  
Brassica Crops ◽  
Model Plant Arabidopsis Thaliana ◽  
Vernalization Pathway

Flowering time is a key agronomic trait, directly influencing crop yield and quality. Many flowering-time genes have been identified and characterized in the model plant Arabidopsis thaliana; however, these genes remain uncharacterized in many agronomically important Brassica crops. In this study, we identified 1064, 510, and 524 putative orthologs of A. thaliana flowering-time genes from Brassica napus, Brassica rapa, and Brassica oleracea, respectively, and found that genes involved in the aging and ambient temperature pathways were fewer than those in other flowering pathways. Flowering-time genes were distributed mostly on chromosome C03 in B. napus and B. oleracea, and on chromosome A09 in B. rapa. Calculation of non-synonymous (Ka)/synonymous substitution (Ks) ratios suggested that flowering-time genes in vernalization pathways experienced higher selection pressure than those in other pathways. Expression analysis showed that most vernalization-pathway genes were expressed in flowering organs. Approximately 40% of these genes were highly expressed in the anther, whereas flowering-time integrator genes were expressed in a highly organ-specific manner. Evolutionary selection pressures were negatively correlated with the breadth and expression levels of vernalization-pathway genes. These findings provide an integrated framework of flowering-time genes in these three Brassica crops and provide a foundation for deciphering the relationship between gene expression patterns and their evolutionary selection pressures in Brassica napus.

Development of amplified consensus genetic markers (ACGM) in Brassica napus from Arabidopsis thaliana sequences of known biological function

Genome ◽  
1999 ◽  
Vol 42 (3) ◽  
pp. 387-402 ◽  
Author(s):  
Dominique Brunel ◽  
Nicole Froger ◽  
Georges Pelletier
Keyword(s):  
Arabidopsis Thaliana ◽  
Brassica Napus ◽  
Genetic Markers ◽  
Biological Function ◽  
Parental Species ◽  
Direct Sequencing ◽  
Brassica Species ◽  
Degenerate Primers ◽  
Coding Sequences ◽  
Pcr Products

A method for the development of consensus genetic markers between species of the same taxonomic family is described in this paper. It is based on the conservation of the peptide sequences and on the potential polymorphism within non-coding sequences. Six loci sequenced from Arabidopsis thaliana, AG, LFY3, AP3, FAD7, FAD3, and ADH, were analysed for one ecotype of A. thaliana, four lines of Brassica napus, and one line for each parental species, Brassica oleracea and Brassica rapa. Positive amplifications with the degenerate primers showed one band for A. thaliana, two to four bands in rapeseed, and one to two bands in the parental species. Direct sequencing of the PCR products confirms their peptide similarity with the "mother" sequence. By comparison of intron sequences, the correspondence between each rapeseed gene and its homologue in one of the parental species can be determined without ambiguity. Another important result is the presence of a polymorphism inside these fragments between the rapeseed lines. This variability could generally be detected by differences of electrophoretic migration on long non-denaturing polyacrylamide gels. This method enables a quick and easy shuttle between A. thaliana and Brassica species without cloning.Key words: consensus genetics markers, PCR specific, Brassica, Arabidopsis, targeted markers, DSCP.

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