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Huang Y, Huang X, Zhou X, Wang J, Zhang R, Ma F, Wang K, Zhang Z, Dai X, Cao X, Zhang C, Han K, Ren Q. Immune activation by a multigene family of lectins with variable tandem repeats in oriental river prawn ( Macrobrachium nipponense). Open Biol 2020; 10:200141. [PMID: 32931720 PMCID: PMC7536079 DOI: 10.1098/rsob.200141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Genomic regions with repeated sequences are unstable and prone to rapid DNA diversification. However, the role of tandem repeats within the coding region is not fully characterized. Here, we have identified a new hypervariable C-type lectin gene family with different numbers of tandem repeats (Rlecs; R means repeat) in oriental river prawn (Macrobrachium nipponense). Two types of repeat units (33 or 30 bp) are identified in the second exon, and the number of repeat units vary from 1 to 9. Rlecs can be classified into 15 types through phylogenetic analysis. The amino acid sequences in the same type of Rlec are highly conservative outside the repeat regions. The main differences among the Rlec types are evident in exon 5. A variable number of tandem repeats in Rlecs may be produced by slip mispairing during gene replication. Alternative splicing contributes to the multiplicity of forms in this lectin gene family, and different types of Rlecs vary in terms of tissue distribution, expression quantity and response to bacterial challenge. These variations suggest that Rlecs have functional diversity. The results of experiments on sugar binding, microbial inhibition and clearance, regulation of antimicrobial peptide gene expression and prophenoloxidase activation indicate that the function of Rlecs with the motif of YRSKDD in innate immunity is enhanced when the number of tandem repeats increases. Our results suggest that Rlecs undergo gene expansion through gene duplication and alternative splicing, which ultimately leads to functional diversity.
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Affiliation(s)
- Ying Huang
- College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu 210023, People's Republic of China.,College of Oceanography, Hohai University, 1 Xikang Road, Nanjing, Jiangsu 210098, People's Republic of China
| | - Xin Huang
- College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu 210023, People's Republic of China
| | - Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Jialin Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Ruidong Zhang
- College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu 210023, People's Republic of China
| | - Futong Ma
- College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu 210023, People's Republic of China
| | - Kaiqiang Wang
- College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu 210023, People's Republic of China
| | - Zhuoxing Zhang
- College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu 210023, People's Republic of China
| | - Xiaoling Dai
- College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu 210023, People's Republic of China
| | - Xueying Cao
- College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu 210023, People's Republic of China
| | - Chao Zhang
- College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu 210023, People's Republic of China
| | - Keke Han
- College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu 210023, People's Republic of China
| | - Qian Ren
- College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, Jiangsu 210023, People's Republic of China.,Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, People's Republic of China
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Abstract
Intron sequences in nuclear pre-mRNAs are excised with either the major U2 snRNA-dependent spliceosomal pathway or the minor U12 snRNA-dependent spliceosomal pathway that exist in most eukaryotic organisms. While the predominant dinucleotides bordering each of these types of introns and the catalytic mechanism used in their excision are conserved in plants and animals, several features aiding in the recognition of plant introns are distinct from those in animals and yeast. Along with their short length, high AU content and high variation in their 5' and 3' splice sites and branchpoint consensus sequences are the most prominent characteristics of plant introns. Detailed surveys of site-directed mutant introns tested in vivo and chemically induced and naturally mutant introns analyzed in planta emphasize the effects of changing individual nucleotides in these splice site consensus sequences and highlight a number of noncanonical dinucleotides that are functional in plant systems.
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Affiliation(s)
- M A Schuler
- Department of Cell and Developmental Biology, University of Illinois, Urbana, IL 61801, USA.
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3
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Viquez OM, Konan KN, Dodo HW. Genomic organization of peanut allergen gene, Ara h 3. Mol Immunol 2005; 41:1235-40. [PMID: 15482859 DOI: 10.1016/j.molimm.2004.06.033] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2004] [Accepted: 06/09/2004] [Indexed: 11/19/2022]
Abstract
Type 1 hypersensitivity to peanut proteins is a well-recognized health problem. Several peanut seed storage proteins have been identified as allergens. Ara h 3, a glycinin protein, is one of the important peanut allergens. Although amino acid and cDNA sequences are available for Ara h 3, there is not information at the genomic level. The objectives of this study were to isolate, sequence, and characterize the genomic clone of peanut allergen, Ara h 3. A peanut genomic library was screened, using two [32P] end-labeled oligonucleotide probes designed based on cDNA sequences of Ara h 3 and Ara h 4. Four positives lambda FIX II clones were obtained after four rounds of screenings. Digestion with Sac I resulted in two fragments of 1.5 and 10 kb hybridizing to the probes. Both fragments were subcloned into p-Bluescript vector and sequenced. The Ara h 3 gene spans 3.5 kb and consists of four exons, three introns, 5' and 3' flanking regions. The open reading frame is 2008 bp long and can encode a polypeptide of 538 amino acids residues. Sequences analogous to a TATA-box (TATAAAT), CAAT-box (AGGA), G-box (TCCTACGTGTCC) and several cis-elements were found in the promoter region. In the 3' downstream region, three polyadenylation signals (AATAAA) were identified.
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Affiliation(s)
- Olga M Viquez
- Food Biotechnology Laboratory, Department of Food and Animal Sciences, P.O. Box 1628, Alabama A and M University, Normal AL 35762, USA
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Lazarova DL, Spengler BA, Biedler JL, Ross RA. HuD, a neuronal-specific RNA-binding protein, is a putative regulator of N-myc pre-mRNA processing/stability in malignant human neuroblasts. Oncogene 1999; 18:2703-10. [PMID: 10348344 DOI: 10.1038/sj.onc.1202621] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
N-myc gene copy numbers and transcription rates are similar in N (neuroblastic, tumorigenic) and S (non-neuronal, non-tumorigenic) neuroblastoma cells with chromosomally integrated amplified N-myc genes. However, N cells show significantly higher N-myc mRNA levels than S cells. Therefore, post-transcriptional control of N-myc gene expression must differ between these cell types. Since no differences in N-myc mRNA half-life were found between N and S cells from two cell lines, steady-state levels of N-myc pre-mRNA processing intermediates were analysed. Results suggest that the differences in N-myc expression arise primarily at the nuclear post-transcriptional level. The neuronal-specific RNA-binding Hu proteins are present in cytoplasmic and nuclear fractions of N cells and one of them, HuD, binds specifically to both exonic and intronic N-myc RNA sequences. In sense and antisense HuD-transfected N cells, there are coordinate changes in HuD and N-myc expression levels. Thus, we propose that HuD plays a role in the nuclear processing/stability of N-myc pre-mRNA in N-type neuroblastoma cells.
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Affiliation(s)
- D L Lazarova
- Department of Biological Sciences, Fordham University, Bronx, New York 10458, USA
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Frances H, Bligh J, Larkin PD, Roach PS, Jones CA, Fu H, Park WD. Use of alternate splice sites in granule-bound starch synthase mRNA from low-amylose rice varieties. PLANT MOLECULAR BIOLOGY 1998; 38:407-15. [PMID: 9747848 DOI: 10.1023/a:1006021807799] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The rice Waxy gene encodes a granule-bound starch synthase (GBSS) necessary for the synthesis of amylose in endosperm tissue. We have previously shown that a CT microsatellite near the transcriptional start site of the GBSS gene can distinguish 7 alleles that accounted for more than 80% of the variation in apparent amylose content in an extended pedigree of 89 US rice cultivars (Oryza sativa L.). Furthermore, all the cultivars with 18% or less amylose were shown to have the sequence AGTTATA at the putative leader intron 5' splice site, while all cultivars with a higher proportion of amylose had AGGTATA. Here we demonstrate that this single-base mutation reduces the efficiency of GBSS pre-mRNA processing and results in alternate splicing at three cryptic sites. The predominant 5' splice site in CT18 low-amylose varieties is 93 bp upstream of the splice site used in intermediate and high amylose varieties and is immediately 5' to the CT microsatellite that we previously demonstrated to be tightly correlated with amylose content. Use of the leader intron 5' splice site at either -93 or -1 in conjunction with the predominant 3' splice site results in formation of a small open reading frame 38 bp upstream of the normal ATG and out of frame with it. This open reading frame is not produced when any of the 5' leader intron splice sites are used in conjunction with an alternate 3' splice site five bases further downstream which was observed in all rice varieties tested.
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Affiliation(s)
- H Frances
- Department of Biochemistry, Queens Medical Centre, University of Nottingham, UK
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Isshiki M, Morino K, Nakajima M, Okagaki RJ, Wessler SR, Izawa T, Shimamoto K. A naturally occurring functional allele of the rice waxy locus has a GT to TT mutation at the 5' splice site of the first intron. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 1998; 15:133-8. [PMID: 9744101 DOI: 10.1046/j.1365-313x.1998.00189.x] [Citation(s) in RCA: 150] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
In cultivated rice two wild-type alleles, Wxa and Wxb, predominate at the waxy locus, which encodes granule-bound starch synthase. The activity of Wxa is 10-fold higher than that of Wxb at the level of both protein and mRNA. Wxb has a +1G to T mutation at the 5' splice site of the first intron. Sequence analysis of Wxb transcripts revealed that splicing occurs at the mutant AG/UU site and at two cryptic sites: the first is A/GUU, one base upstream of the original site and the second is AG/GU found approximately 100 bases upstream of the mutant splice site. We introduced single base mutations to the 5' splice sites of both Wxa and Wxb, fused with the gus reporter gene and introduced them into rice protoplasts. Analysis of GUS activities and transcripts indicated that a G to T mutation in Wxa reduced GUS activity and the level of spliced RNA. Conversely, a T to G mutation of Wxb restored GUS activity and the level of spliced RNA to that of wild-type Wxa. These results demonstrated that the low level expression of Wxb results from a single base mutation at the 5' splice site of the first intron. It is of interest that the Wxb allele of rice carrying the G to T mutation of intron 1 has been conserved in the history of rice cultivation because there is a low amylose content of the seed caused by this mutation.
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Affiliation(s)
- M Isshiki
- Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, Takayama, Japan
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7
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Mutation pressure, natural selection, and the evolution of base composition in Drosophila. ACTA ACUST UNITED AC 1998. [DOI: 10.1007/978-94-011-5210-5_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2023]
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Standiford DM, Davis MB, Sun W, Emerson CP. Splice-junction elements and intronic sequences regulate alternative splicing of the Drosophila myosin heavy chain gene transcript. Genetics 1997; 147:725-41. [PMID: 9335608 PMCID: PMC1208193 DOI: 10.1093/genetics/147.2.725] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The Drosophila muscle myosin heavy chain (Mhc) gene primary transcript contains five alternatively spliced exon groups (exon 3, 7, 9, 11 and 15), each of which contains two to five mutually exclusive members. Individual muscles typically select a specific alternative exon from each group for incorporation into the processed message. We report here on the cis-regulatory mechanisms that direct the processing of alternative exons in Mhc exon 11 in individual muscles using transgenic reporter constructs, RT-PCR and directed mutagenesis. The 6.0-kilobase exon 11 domain is sufficient to direct the correct processing of exon 11 alternatives, demonstrating that the alternative splicing cis-regulatory elements are local to Mhc exon 11. Mutational analysis of Mhc exon 11 reveals that the alternative exon nonconsensus 5'-splice donors are essential for alternative splicing regulation in general, but do not specify alternative exons for inclusion in individual muscles. Rather, we show, through exon substitutions and deletion analyses, that a 360-nucleotide intronic domain precisely directs the normal processing of one exon, Mhc exon 11e, in the indirect flight muscle. These and other data indicate that alternative exons are regulated in appropriate muscles through interactions between intronic alternative splice-specificity elements, nonconsensus exon 11 splice donors and, likely, novel exon-specific alternative splicing factors.
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Affiliation(s)
- D M Standiford
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia 19104-6058, USA
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Okano HJ, Darnell RB. A hierarchy of Hu RNA binding proteins in developing and adult neurons. J Neurosci 1997; 17:3024-37. [PMID: 9096138 PMCID: PMC6573636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/1996] [Revised: 02/03/1997] [Accepted: 02/11/1997] [Indexed: 02/04/2023] Open
Abstract
The Hu proteins are a group of antigens targeted in an immune-mediated neurodegenerative disorder associated with cancer. We have cloned and characterized four members of the Hu gene family from mouse. We find that the Hu genes encode a large number of alternatively spliced transcripts to produce a series of related neuron-specific RNA binding proteins. Despite this complexity, we have discerned several ordered features of Hu expression. In the embryo, specific Hu genes are expressed in a hierarchy during early neurogenesis. In the E16 developing cortex, mHuB is induced in very early postmitotic neurons exiting the ventricular zone, mHuD is expressed in migrating neurons of the intermediate zone, and mHuC is expressed in mature cortical plate neurons. Such a hierarchy suggests distinct functional roles for each gene in developing neurons. In the adult, all neurons express some set of Hu mRNA and protein. However, specific patterns are evident such that individual neuronal types in the hippocampus, cerebellum, olfactory cortex, neocortex, and elsewhere express from one to several Hu genes. The complexity of potential protein variants within a gene family and of different Hu family members within a neuron suggests a diverse array of function. Given the strong homologies among the Hu proteins, the Drosophila neurogenic gene elav, and the Drosophila splicing factor sxl, we predict that different combinations of Hu proteins determine different neuron-specific aspects of post-transcriptional RNA regulation. Our findings of specific developmental patterns of expression and the correlation between immune targeting of the Hu proteins and adult neurodegenerative disease suggest that the Hu proteins are critical in both the proper development and function of mature neurons.
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Affiliation(s)
- H J Okano
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10021, USA
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McCullough AJ, Schuler MA. Intronic and exonic sequences modulate 5' splice site selection in plant nuclei. Nucleic Acids Res 1997; 25:1071-7. [PMID: 9023120 PMCID: PMC146543 DOI: 10.1093/nar/25.5.1071] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Pre-mRNA transcripts in a variety of organisms, including plants, Drosophila and Caenorhabditis elegans, contain introns which are significantly richer in adenosine and uridine residues than their flanking exons. Previous analyses using exonic and intronic replacements between two nonequivalent 5'splice sites in the 469 nt long rbcS3A intron 1 provided the first evidence indicating that, in both tobacco and Drosophila nuclei, 5'splice site selection is strongly influenced by the position of that site relative to the AU transition point between exon and intron. To differentiate between two potential models for 5'splice site recognition, we have expressed a completely different set of intronic and exonic replacement constructs containing identical 5'splice sites upstream of beta-conglycinin intron 4 (115 nt). Mutagenesis and deletion of the upstream 5'splice site demonstrate that intronic AU-rich sequences function by promoting recognition of the most upstream 5'splice site rather than by masking the downstream 5'splice site. Sequence insertions define a role for AG-rich exonic sequences in plant pre-mRNA splicing by demonstrating that an AG-rich element is capable of promoting downstream 5'splice site recognition. We conclude that AU-rich intronic sequences, AG-rich exonic sequences and the 5'splice site itself collectively define 5'intron boundaries in dicot nuclei.
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Affiliation(s)
- A J McCullough
- Verna and Marrs McClean Department of Biochemistry, Baylor College of Medicine, Houston, TX 77030, USA
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McCullough AJ, Baynton CE, Schuler MA. Interactions across exons can influence splice site recognition in plant nuclei. THE PLANT CELL 1996; 8:2295-307. [PMID: 8989884 PMCID: PMC161353 DOI: 10.1105/tpc.8.12.2295] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
In vivo analyses of cis-acting sequence requirements for pre-mRNA splicing in tobacco nuclei have previously demonstrated that the 5' splice sites are selected by their position relative to AU-rich elements within plant introns and by their degree of complementarity to the U1 small nuclear RNA. To determine whether the presence of adjacent introns affects 5' splice site recognition in plant nuclei, we have analyzed the in vivo splicing patterns of two-intron constructs containing 5' splice site mutations in the second intron. These experiments indicated that the splice site selection patterns in plant nuclei are defined primarily by sequences within the intron (intron definition) and secondarily by weak interactions across exons (exon definition). The effects of these secondary interactions became evident only when mutations in the downstream 5' splice site decreased its functionality and differed depending on the availability of cryptic splice sites close to the mutant site. In beta-conglycinin chimeric transcripts containing multiple cryptic 5' splice sites, the presence of an intact upstream intron significantly increased splicing at the downstream 5' splice sites in a polar fashion without activating exon skipping. In a natural beta-conglycinin transcript, which does not contain cryptic 5'splice sites, mutation of the first nucleotide of the downstream intron activated an array of noncanonical 5' and 3' splice sites and some exon skipping.
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Affiliation(s)
- A J McCullough
- Department of Plant Biology, University of Illinois, Urbana 61801, USA
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Pret AM, Fiszman MY. Sequence divergence associated with species-specific splicing of the nonmuscle beta-tropomyosin alternative exon. J Biol Chem 1996; 271:11511-7. [PMID: 8626711 DOI: 10.1074/jbc.271.19.11511] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Alternative splicing of vertebrate beta-tropomyosin transcripts ensures mutually exclusive expression of internal exons 6A and 6B in nonmuscle and skeletal muscle cells, respectively. Recently, we reported that this splicing regulation requires species-specific elements, since the splicing profile for the chicken, rat, and Xenopus beta-tropomyosin alternative exons is not reproduced in transfection experiments when heterologous myogenic cells are used. By analyzing the splicing pattern of hybrid chicken/rat beta-TM constructions transfected into both quail and mouse cell lines, we demonstrate that chicken beta-tropomyosin exon 6A is flanked by stronger splicing signals than rat exon 6A, thus leading to the misregulation of splicing in heterologous cells. We have characterized three splicing signals that contribute to this difference: 1) nonconsensus nucleotide differences at positions +4 and +6 in the donor site downstream of exon 6A, 2) differences in the pyrimidine composition between the branch site and acceptor site upstream of exon 6A, and 3) a pyrimidine-rich intronic exon 6A splicing enhancer present upstream of exon 6A only in the chicken beta-TM gene. The functional divergence between splicing signals in two homologous vertebrate genes reveals species-specific strategies for proper modulation of splicing of alternative exons.
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Affiliation(s)
- A M Pret
- Department of Molecular Biology, Pasteur Institute, Paris, France
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