Isolation of Lhcb3 sequences from Brassica napus: evidence for conserved genes encoding LHCII type III chlorophyll a/b binding proteins

Genome ◽  
1993 ◽  
Vol 36 (1) ◽  
pp. 139-146 ◽  
Author(s):  
Rodolphe Boivin ◽  
Diane Beauseigle ◽  
Chris L. Baszczynski ◽  
Guy Bellemare
Keyword(s):  
Brassica Napus ◽  
Chlorophyll A ◽  
Binding Proteins ◽  
Specific Binding ◽  
Evolutionary Relationship ◽  
Upstream Region ◽  
Type I ◽  
Mobility Shift ◽  
Type Iii ◽  
Genes Encoding

Three closely related sequences were isolated from Brassica napus genomic DNA and were identified as Lhcb3 (genes encoding type III chlorophyll a/b binding proteins of LHCII, the major light-harvesting complex of photosystem II). These genes, as was observed for a tomato Lhcb3, contain two introns and yield both divergent and conserved predicted amino acid segments as compared with type I and type II polypeptides. One of the B. napus genes, designated Lhcb3*1, is transcribed in vivo, since it is identical to corresponding sequences in a cDNA clone. The protein deduced from another sequence, Lhcb3*2, appears as the most divergent type III so far characterized. The partial sequence of a third gene, Lhcb3*3, was also recovered. The 5′ noncoding sequences of Lhcb3*1 and Lhcb3*2, in the far upstream region, are characterized by an extremely high AT content and extensive direct repeats. In the near upstream region, two long Lhcb3*2 segments are very similar to a segment proposed as containing regulatory signals in Lhcb3*1. Specific binding of nuclear proteins to Lhcb3*1 promoter fragments was detected by electrophoretic mobility-shift assays. The evolutionary relationship between genes for type III polypeptides and the other types present in LHCII is discussed.Key words: Brassica napus, chlorophyll a/b binding proteins, LHCII type III, promoter region, lhcb genes evolution.

scholarly journals Insights into the ancestry evolution of the Mycobacterium tuberculosis complex from analysis of Mycobacterium riyadhense

2021 ◽  
Vol 3 (3) ◽  
Author(s):  
Qingtian Guan ◽  
Musa Garbati ◽  
Sara Mfarrej ◽  
Talal AlMutairi ◽  
Thomas Laval ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Mycobacterium Tuberculosis Complex ◽  
Evolutionary Relationship ◽  
Type I ◽  
Dna Sensors ◽  
Mycobacterial Species ◽  
Tuberculosis Complex ◽  
Genes Encoding ◽  
Cumulative Process ◽  
Comparative Transcriptomic Analysis

Abstract Current evolutionary scenarios posit the emergence of Mycobacterium tuberculosis from an environmental saprophyte through a cumulative process of genome adaptation. Mycobacterium riyadhense, a related bacillus, is being increasingly isolated from human clinical cases with tuberculosis-like symptoms in various parts of the world. To elucidate the evolutionary relationship between M. riyadhense and other mycobacterial species, including members of the M. tuberculosis complex (MTBC), eight clinical isolates of M. riyadhense were sequenced and analyzed. We show, among other features, that M. riyadhense shares a large number of conserved orthologs with M. tuberculosis and shows the expansion of toxin/antitoxin pairs, PE/PPE family proteins compared with other non-tuberculous mycobacteria. We observed M. riyadhense lacks wecE gene which may result in the absence of lipooligosaccharides (LOS) IV. Comparative transcriptomic analysis of infected macrophages reveals genes encoding inducers of Type I IFN responses, such as cytosolic DNA sensors, were relatively less expressed by macrophages infected with M. riyadhense or M. kansasii, compared to BCG or M. tuberculosis. Overall, our work sheds new light on the evolution of M. riyadhense, its relationship to the MTBC, and its potential as a system for the study of mycobacterial virulence and pathogenesis.

Genes encoding light-harvesting chlorophyll a/b-binding proteins in papaya (Carica papaya L.) and insight into lineage-specific evolution in Brassicaceae

Gene ◽  
2020 ◽  
Vol 748 ◽  
pp. 144685
Author(s):  
Zhi Zou ◽  
Meiying Li ◽  
Ruizong Jia ◽  
Hui Zhao ◽  
Pingping He ◽  
...  
Keyword(s):  
Chlorophyll A ◽  
Binding Proteins ◽  
Carica Papaya ◽  
Light Harvesting ◽  
Genes Encoding ◽  
Insight Into

scholarly journals Insights Into the Molecular Evolution of AT-Hook Motif Nuclear Localization Genes in Brassica napus

2021 ◽  
Vol 12 ◽  
Author(s):  
Wei-Meng Zhang ◽  
Da Fang ◽  
Xiu-Zhu Cheng ◽  
Jun Cao ◽  
Xiao-Li Tan
Keyword(s):  
Brassica Napus ◽  
Plant Growth ◽  
Gene Family ◽  
Nuclear Localization ◽  
Growth And Development ◽  
Gene Organization ◽  
Type I ◽  
Type Ii ◽  
Plant Growth And Development ◽  
Type Iii

AT-hook motif nuclear localization (AHL) proteins belong to a family of transcription factors, and play important roles in plant growth and development and response to various stresses through protein-DNA and protein-protein interactions. To better understand the Brassica napus AHL gene family, AHL genes in B. napus and related species were analyzed. Using Arabidopsis as a reference, 122 AHL gene family members were first identified in B. napus. According to the phylogenetic tree and gene organization, the BnaAHLs were classified into two clades (Clade-A and Clade-B) and three types (Type-I, Type-II, and Type-III). Gene organization and motif distribution analysis suggested that the AHL gene family is relatively conserved during evolution. These BnaAHLs are unevenly distributed on 38 chromosomes and expanded by whole-genome duplication (WGD) or segmental duplication. And large-scale loss events have also occurred in evolution. All types of BnaAHLs are subject to purification or neutral selection, while some positive selection sites are also identified in Type-II and Type-III groups. At the same time, the purification effect of Type-I members are stronger than that of the others. In addition, RNA-seq data and cis-acting element analysis also suggested that the BnaAHLs play important roles in B. napus growth and development, as well as in response to some abiotic and biotic stresses. Protein-protein interaction analysis identified some important BnaAHL-binding proteins, which also play key roles in plant growth and development. This study is helpful to fully understand the origin and evolution of the AHL gene in B. napus, and lays the foundation for their functional studies.

Promoter activity of the proliferating-cell nuclear antigen gene is associated with inducible CRE-binding proteins in interleukin 2-stimulated T lymphocytes

1994 ◽  
Vol 14 (6) ◽  
pp. 4233-4243
Author(s):  
D Huang ◽  
P M Shipman-Appasamy ◽  
D J Orten ◽  
S H Hinrichs ◽  
M B Prystowsky
Keyword(s):  
Proliferating Cell Nuclear Antigen ◽  
Promoter Activity ◽  
Binding Proteins ◽  
Specific Binding ◽  
Interleukin 2 ◽  
Nuclear Antigen ◽  
Promoter Strength ◽  
Proliferating Cells ◽  
Mobility Shift ◽  
Proliferating Cell

The proliferating-cell nuclear antigen (PCNA) gene encodes an auxiliary factor of DNA polymerase delta and functions in DNA replication during S phase. It is expressed at much higher levels in proliferating cells than in quiescent cells. We have studied the regulatory role of the 5'-flanking sequence of the murine PCNA gene in interleukin 2 (IL-2)-responsive cloned T cells (L2). Analysis of a set of deletion constructs in transient transfection assays measuring heterologous reporter gene (luciferase) activity demonstrated that the 182-bp 5'-flanking region provides full promoter activity in IL-2-stimulated L2 cells. While many elements contribute to PCNA promoter strength in IL-2-stimulated cells, the largest decrease in activity occurred with deletion of the tandem CRE (cyclic AMP response element) binding sites located at nucleotides -37 to -52. With a gel mobility shift assay, several IL-2-inducible DNA-protein complexes were detected, including CREB (CRE-binding) and ATF1 (activating transcription factor) proteins that are specific for the PCNA-CRE sequence. Methylation interference analysis confirmed specific binding of these proteins to the CRE sites. Mutation at the PCNA-CRE motif abolishes IL-2-inducible binding and reduces substantially PCNA promoter activity. These results indicate that IL-2-stimulated PCNA transcription may be partially mediated by these CRE-binding proteins.

scholarly journals Cloning and characterization of the 5′-flanking region of the oxalate decarboxylase gene from Flammulina velutipes

2002 ◽  
Vol 367 (1) ◽  
pp. 67-75 ◽  
Author(s):  
Mohammad AZAM ◽  
Meenu KESARWANI ◽  
Subhra CHAKRABORTY ◽  
Krishnamurthy NATARAJAN ◽  
Asis DATTA
Keyword(s):  
Transcription Factor ◽  
Oxalic Acid ◽  
Specific Binding ◽  
Low Ph ◽  
Flammulina Velutipes ◽  
Upstream Region ◽  
Oxalate Decarboxylase ◽  
Mobility Shift ◽  
Cell Extracts ◽  
Flanking Region

The oxalate-degrading enzyme, oxalate decarboxylase (OXDC), was purified and characterized from Flammulina velutipes, a basidiomycetous fungus [Mehta and Datta (1991) J. Biol. Chem. 266, 23548—23553]. The cDNA cloning and analyses revealed that OXDC transcription was induced by oxalic acid. However, in this report, we show that OXDC transcription is induced by low pH, not by oxalate. To understand the regulatory mechanism of OXDC expression, we have cloned and analysed a 580-bp genomic fragment from the 5′-flanking region of the OXDC gene. Sequence analysis showed the presence of several eukaryotic transcription factor binding motifs within the −580bp of the upstream region. Electrophoretic-mobility-shift assays with partially purified cell extracts revealed specific binding of a factor in acid-induced, but not in uninduced, extracts. Furthermore, DNase I protection assays using the partially purified fraction from oxalic acid-induced extract revealed a footprint of a 13-bp sequence 5′GCGGGGTCGCCGA3′, termed low pH responsive element (LPRE), corresponding to the −287 to −275bp region of the OXDC promoter. Our results suggest that in F. velutipes cells, activation of OXDC transcription in response to low pH is mediated by the binding of a novel transcription factor through the LPRE site in the OXDC promoter.

Molecular characterization and genetic mapping of two clusters of genes encoding chlorophyll a/b-binding proteins in Lycopersicon esculentum (tomato)

Gene ◽  
1985 ◽  
Vol 40 (2-3) ◽  
pp. 247-258 ◽  
Author(s):  
Eran Pichersky ◽  
Robert Bernatzky ◽  
Steven D. Tanksley ◽  
R.Bill Breidenbach ◽  
Albert P. Kausch ◽  
...  
Keyword(s):  
Lycopersicon Esculentum ◽  
Genetic Mapping ◽  
Molecular Characterization ◽  
Chlorophyll A ◽  
Binding Proteins ◽  
Genes Encoding

scholarly journals Antigenic and Sequence Diversity in Gonococcal Transferrin-Binding Protein A

2000 ◽  
Vol 68 (8) ◽  
pp. 4725-4735 ◽  
Author(s):  
Cynthia Nau Cornelissen ◽  
James E. Anderson ◽  
Ian C. Boulton ◽  
P. Frederick Sparling
Keyword(s):  
Synthetic Peptides ◽  
Pathogenic Bacteria ◽  
Binding Proteins ◽  
Specific Binding ◽  
Protein A ◽  
Sequence Diversity ◽  
Western Blots ◽  
Gram Negative ◽  
Genes Encoding ◽  
Transferrin Binding Proteins

ABSTRACT Neisseria gonorrhoeae is a gram-negative pathogen that is capable of satisfying its iron requirement with human iron-binding proteins such as transferrin and lactoferrin. Transferrin-iron utilization involves specific binding of human transferrin at the cell surface to what is believed to be a complex of two iron-regulated, transferrin-binding proteins, TbpA and TbpB. The genes encoding these proteins have been cloned and sequenced from a number of pathogenic, gram-negative bacteria. In the current study, we sequenced four additional tbpA genes from other N. gonorrhoeaestrains to begin to assess the sequence diversity among gonococci. We compared these sequences to those from other pathogenic bacteria to identify conserved regions that might be important for the structure and function of these receptors. We generated polyclonal mouse sera against synthetic peptides deduced from the TbpA sequence from gonococcal strain FA19. Most of these synthetic peptides were predicted to correspond to surface-exposed regions of TbpA. We found that, while most reacted with denatured TbpA in Western blots, only one antipeptide serum reacted with native TbpA in the context of intact gonococci, consistent with surface exposure of the peptide to which this serum was raised. In addition, we evaluated a panel of gonococcal strains for antigenic diversity using these antipeptide sera.

scholarly journals Promoter activity of the proliferating-cell nuclear antigen gene is associated with inducible CRE-binding proteins in interleukin 2-stimulated T lymphocytes.

1994 ◽  
Vol 14 (6) ◽  
pp. 4233-4243 ◽  
Author(s):  
D Huang ◽  
P M Shipman-Appasamy ◽  
D J Orten ◽  
S H Hinrichs ◽  
M B Prystowsky
Keyword(s):  
Proliferating Cell Nuclear Antigen ◽  
Promoter Activity ◽  
Binding Proteins ◽  
Specific Binding ◽  
Interleukin 2 ◽  
Nuclear Antigen ◽  
Promoter Strength ◽  
Proliferating Cells ◽  
Mobility Shift ◽  
Proliferating Cell

The proliferating-cell nuclear antigen (PCNA) gene encodes an auxiliary factor of DNA polymerase delta and functions in DNA replication during S phase. It is expressed at much higher levels in proliferating cells than in quiescent cells. We have studied the regulatory role of the 5'-flanking sequence of the murine PCNA gene in interleukin 2 (IL-2)-responsive cloned T cells (L2). Analysis of a set of deletion constructs in transient transfection assays measuring heterologous reporter gene (luciferase) activity demonstrated that the 182-bp 5'-flanking region provides full promoter activity in IL-2-stimulated L2 cells. While many elements contribute to PCNA promoter strength in IL-2-stimulated cells, the largest decrease in activity occurred with deletion of the tandem CRE (cyclic AMP response element) binding sites located at nucleotides -37 to -52. With a gel mobility shift assay, several IL-2-inducible DNA-protein complexes were detected, including CREB (CRE-binding) and ATF1 (activating transcription factor) proteins that are specific for the PCNA-CRE sequence. Methylation interference analysis confirmed specific binding of these proteins to the CRE sites. Mutation at the PCNA-CRE motif abolishes IL-2-inducible binding and reduces substantially PCNA promoter activity. These results indicate that IL-2-stimulated PCNA transcription may be partially mediated by these CRE-binding proteins.

scholarly journals Expression of collagens in the damage area at abdominal adhesions

2017 ◽  
Vol 2 (6) ◽  
pp. 188-192
Author(s):  
Irina Shurygina ◽  
Irina Shurygina ◽  
Mikhail Shurygin ◽  
Mikhail Shurygin ◽  
Lyubov Rodionova ◽  
...  
Keyword(s):  
Abdominal Cavity ◽  
Immunofluorescent Staining ◽  
Type Iii Collagen ◽  
Type I ◽  
Damage Area ◽  
Type Iii ◽  
Expression Of Genes ◽  
Genes Encoding ◽  
Type V ◽  
Adhesion Process

Background. Postoperative adhesions are a serious problem in surgery. However, at the present time molecular mechanisms of the adhesion process are insufficiently studied. Aim. To study the dynamics of expression of genes encoding the synthesis of collagen in case of damage to the serosa on the example of the peritoneum in conditions of aseptic inflammation. Materials and methods. Aseptic inflammatory process in the abdominal cavity was modeled (Wistar rats, n = 40). A micro- and macroscopic picture of the damage area was studied. Immunofluorescent staining for Type I collagen (Col 1A1) was performed. The expression of genes encoding collagen of different types was evaluated using the RT 2 - Profiler PCR kit Array Rat Wound Healing. Results. It has been established that the adhesion process with peritoneal damage in aseptic conditions reaches its maximum by the 30 th day of observation. The same period coincides with the maximum of collagen synthesis in fibro- blasts in the repair area, revealed by immunofluorescence study. The interrelation of synthesis of type I and III collagens went as expected – the onset of expression of type III collagen (from day 3) is ahead of the expression of collagen type I (from day 7). Peak gene expression of collagens type I, Alpha-1 and -2; type III Alpha-1, type IV Alpha-1 and -3, type V Alpha-1, -2 and -3; type XIV Alpha-1 (Col14a1) falls on the 14th day. For the first time, active involvement of type V alpha-3 collagen in the adhesion process was noted - we detected both early (from day 1) and maximum intensive (up to 166.96 times increase in comparison with intact animals). Conclusion. Perhaps, the hyperexpression of collagen V alpha-3 that we revealed is an important link in the pathogenesis of adhesion in the abdominal cavity.

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