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Adamopoulos PG, Kontos CK, Scorilas A. Molecular cloning of novel transcripts of human kallikrein-related peptidases 5, 6, 7, 8 and 9 (KLK5 - KLK9), using Next-generation sequencing. Sci Rep 2017; 7:17299. [PMID: 29229980 PMCID: PMC5725587 DOI: 10.1038/s41598-017-16269-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 08/04/2017] [Indexed: 11/26/2022] Open
Abstract
Alternative splicing of cancer-related genes is a common cellular mechanism accounting for cancer cell transcriptome complexity and affecting cell cycle control, proliferation, apoptosis, angiogenesis, invasion, and metastasis. In this study, we describe the discovery and molecular cloning of thirty novel transcripts of the human KLK5, KLK6, KLK7, KLK8 and KLK9 genes, using 3′ rapid amplification of cDNA ends (3′ RACE) and NGS technology, as well as their expression analysis in many established cell lines, originating from several distinct cancerous and normal tissues. Extensive bioinformatic analysis revealed novel splice variants of these five members of the KLK family, comprising entirely new exons, previously unknown boundaries of the already annotated exons (extensions and truncations) as well as alternative splicing events between these exons. Nested RT-PCR in a panel of human cell lines originating from seventeen cancerous and two normal tissues with the use of variant-specific pairs of primers was carried out for expression analysis of these novel splice variants, and Sanger sequencing of the respective amplicons confirmed our NGS results. Given that some splice variants of KLK family members possess clinical value, novel alternatively spliced transcripts appear as new candidate biomarkers for diagnostic and/or prognostic purposes and as targets for therapeutic strategies.
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Affiliation(s)
- Panagiotis G Adamopoulos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, 15701, Greece
| | - Christos K Kontos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, 15701, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, 15701, Greece.
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2
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Bastan R, Eskandari N, Sabzghabaee AM, Manian M. Serine/Threonine phosphatases: classification, roles and pharmacological regulation. Int J Immunopathol Pharmacol 2015; 27:473-84. [PMID: 25572726 DOI: 10.1177/039463201402700402] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Phosphatases are important enzymes in a variety of biochemical pathways in different cells which they catalyze opposing reactions of phosphorylation and dephosphorylation, which may modulate the function of crucial signaling proteins in different cells. This is an important mechanism in the regulation of intracellular signal transduction pathways in many cells. Phosphatases play a key role in regulating signal transduction. It is known that phosphatases are specific for cleavage of either serine-threonine or tyrosine phosphate groups. To date, numerous compounds have been identified. This paper reviews the classification, roles and pharmacological of protein serine/threonine phosphates.
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Affiliation(s)
- R Bastan
- Department of Human Vaccine, Razi-Karaj Institute, Karaj, Iran
| | - N Eskandari
- Department of Immunology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - A M Sabzghabaee
- Isfahan Clinical Toxicology Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - M Manian
- Department of Immunology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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Lehmann R, Meyer J, Schuemann M, Krause E, Freund C. A novel S3S-TAP-tag for the isolation of T-cell interaction partners of adhesion and degranulation promoting adaptor protein. Proteomics 2010; 9:5288-95. [PMID: 19798671 DOI: 10.1002/pmic.200900294] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The identification of modular units of cellular function is a major goal for proteomic research. Protein complexes represent important building blocks defining functionality and deciphering their composition remains a major challenge. Here, we have designed a new tandem affinity purification (TAP) tag (termed S3S-tag) for the isolation of protein complexes. Specifically, the immune cell protein ADAP that regulates integrin adhesion was fused either C- or N-terminally to the S3S-tag. After retroviral transduction of a vector containing S3S-tagged ADAP and internal ribosomal entry site encoded enhanced green fluorescent protein (eGFP), Jurkat T cells were sorted according to eGFP expression and further selected for expression of TAP-tagged protein close to endogenous levels. The combination of a cleavable S-tag and a Strep-tag II allowed for the isolation of ADAP and associated proteins. Subsequently, stable isotope labeling with amino acids in cell culture-based mass spectrometric analysis was performed to identify potentially specific interaction partners. Co-purification of the known interaction partner Src kinase-associated phosphoprotein of 55 kDa indicates the validity of our approach, while the identification of the ENA/VASP family member EVL, the guanine nucleotide exchange factor GEF-H1 and the adaptor protein DOCK2 corroborates a link between ADAP-mediated integrin regulation and the cytoskeleton.
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Affiliation(s)
- Roland Lehmann
- Leibniz-Institute for Molecular Pharmacology, Berlin, Germany
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Chuman Y, Kurihashi W, Mizukami Y, Nashimoto T, Yagi H, Sakaguchi K. PPM1D430, a novel alternative splicing variant of the human PPM1D, can dephosphorylate p53 and exhibits specific tissue expression. J Biochem 2008; 145:1-12. [PMID: 18845566 DOI: 10.1093/jb/mvn135] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
PPM1D is a PPM1 type protein phosphatase and is induced in response to DNA damage. PPM1D-deficient mice show defects in spermatogenesis and lymphoid cell functions but the mechanisms underlying these phenotypes remain unknown. In our current study, we identify and characterize an alternative splicing variant (denoted PPM1D430) of human PPM1D at both the mRNA and protein level. PPM1D430 comprises the common 420 residues of the known PPM1D protein (PPM1D605) and contains a stretch of PPM1D430-specific 10 amino acids. Semi-quantitative reverse transcription-polymerase chain reaction (RT-PCR) analysis revealed that PPM1D430 mRNA is also induced in response to the genotoxic stress in a p53-dependent manner. In vitro phosphatase analysis and PPM1D430-specific RNA interference analysis further indicated that PPM1D430 can dephosphorylate Ser15 of human p53 both in vitro and in vivo. On the other hand, expression profiling of this gene by RT-PCR analysis of a human tissue cDNA panel revealed that PPM1D430 is expressed exclusively in testes and in leucocytes whereas PPM1D605 is ubiquitous. In addition, PPM1D430 shows a different subcellular localization pattern and protein stability when compared with PPM1D605 under some conditions. Our current findings thus suggest that PPM1D430 may exert specific functions in immune response and/or spermatogenesis.
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Affiliation(s)
- Yoshiro Chuman
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
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Sasaki M, Ohnishi M, Tashiro F, Niwa H, Suzuki A, Miyazaki JI, Kobayashi T, Tamura S. Disruption of the mouse protein Ser/Thr phosphatase 2Cβ gene leads to early pre-implantation lethality. Mech Dev 2007; 124:489-99. [PMID: 17499977 DOI: 10.1016/j.mod.2007.04.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2006] [Revised: 03/17/2007] [Accepted: 04/02/2007] [Indexed: 11/29/2022]
Abstract
Protein phosphatase 2Cbeta (PP2Cbeta) is a member of a family of protein Ser/Thr phosphatases (PP2C) that is composed of at least twelve different gene products. Recent studies have revealed that PP2Cbeta mRNA accumulates in mature sperm, unfertilized metaphase II-arrested oocytes and zygotes, but that the mRNA level then decreases sharply between the early two-cell and eight-cell stages, remaining at low levels during the 16-cell to blastocyst stages of mice. These observations raised the possibility that PP2Cbeta plays a crucial role during gametogenesis, fertilization, and/or early stages of embryonic development. In this study, we employed a gene knockout technique in mice to test this possibility. We found that PP2Cbeta(Delta/wt) mice generate normal mature gametes. However, PP2Cbeta(Delta/Delta) embryos die between the two-cell and eight-cell stages. To our interest, PP2Cbeta(Delta/Delta) ES cells which had been generated by transfecting PP2Cbeta(3lox/3lox) ES cells with Cre-expressing plasmid were viable. In addition, knockdown of PP2Cbeta using siRNA did not affect the proliferation of wild-type ES cells. These observations suggest that relatively high PP2Cbeta expression is specifically required during the early stages of pre-implantation development. The possible mechanisms for the early pre-implantation lethality of PP2Cbeta(Delta/Delta) mice are discussed.
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Affiliation(s)
- Masato Sasaki
- Department of Biochemistry, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryomachi, Aoba-ku, Sendai 980-8575, Japan
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Stern A, Privman E, Rasis M, Lavi S, Pupko T. Evolution of the Metazoan Protein Phosphatase 2C Superfamily. J Mol Evol 2006; 64:61-70. [PMID: 17160364 DOI: 10.1007/s00239-006-0033-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2006] [Accepted: 10/04/2006] [Indexed: 01/22/2023]
Abstract
Members of the protein phosphatase 2C (PP2C) superfamily are Mg(2+)/Mn(2+)-dependent serine/threonine phosphatases, which are essential for regulation of cell cycle and stress signaling pathways in cells. In this study, a comprehensive genomic analysis of all available metazoan PP2C sequences was conducted. The phylogeny of PP2C was reconstructed, revealing the existence of 15 vertebrate families which arose following a series of gene duplication events. Relative dating of these duplications showed that they occurred in two active periods: before the divergence of bilaterians and before vertebrate diversification. PP2C families which duplicated during the first period take part in different signaling pathways, whereas PP2C families which diverged in the second period display tissue expression differences yet participate in similar signaling pathways. These differences were found to involve variation of expression in tissues which show higher complexity in vertebrates, such as skeletal muscle and the nervous system. Further analysis was performed with the aim of identifying the functional domains of PP2C. The conservation pattern across the entire PP2C superfamily revealed an extensive domain of more than 50 amino acids which is highly conserved throughout all PP2C members. Several insertion or deletion events were found which may have led to the specialization of each PP2C family.
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Affiliation(s)
- Adi Stern
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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Miyamoto T, Fiorenza MT, Zhao Y, Hasuike S, Westphal H. Molecular cloning and expression analysis of MPP alpha-2, a novel mouse transcript detected in a differential screen of pituitary libraries. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1577:109-12. [PMID: 12151101 DOI: 10.1016/s0167-4781(02)00293-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We identified a novel isoform transcript, MPP alpha-2, of the mouse Mg(2+)-dependent protein phosphatase (MPP) alpha gene. The amino acid sequence encoded by MPP alpha-2 differs from the previously known MPP alpha-1 sequence only at the carboxyl terminal region. Northern and in situ hybridization analysis revealed differential expression patterns of these two transcripts in the embryo and in the adult organism, suggesting an elaborate regulation of the MPP alpha gene.
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Affiliation(s)
- Toshinobu Miyamoto
- Laboratory of Mammalian Genes and Development, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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De Benedictis L, Polizzi A, Cangiano G, Buttiglione M, Arbia S, Storlazzi CT, Rocchi M, Gennarini G. Alternative promoters drive the expression of the gene encoding the mouse axonal glycoprotein F3/contactin. BRAIN RESEARCH. MOLECULAR BRAIN RESEARCH 2001; 95:55-74. [PMID: 11687277 DOI: 10.1016/s0169-328x(01)00243-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
F3/Contactin is a neuronal glycoprotein which mediates axonal growth control via complex interactions with a number of cell surface or matrix components. As part of this developmental role, its expression undergoes differential regulation during the maturation of definite neuronal populations within the central and peripheral nervous tissue. To elucidate the underlying molecular mechanisms we study here the organization of the regulatory region of the mouse F3/Contactin gene. We show that this region displays peculiar features in that it spans more than 80 kb, bears very large introns and includes four untranslated exons which undergo complex splicing events leading to 11 potential arrangements of the F3/Contactin mRNA 5' end. Within this region we identify three alternative neurospecific promoters which, as deduced from the developmental profile of the associated 5' exons (A1,C1,0), drive two different patterns of F3/Contactin gene expression. The activity of the A1 exon-associated promoter displays only minor developmental changes and is likely to contribute to the basal level of the F3/Contactin gene expression; by contrast, the activities of the exon C1- and exon 0-associated promoters are significantly upregulated at the end of the first postnatal week. The data indicate that differential regulation of the F3/Contactin expression during development may depend upon alternative utilization of distinct promoter elements and may involve complex splicing events of the 5' untranslated exons. Several consensuses for homeogene transcription factors are scattered within the identified regulatory region, in agreement with the general assumption of homeotic gene regulation of neural morphoregulatory molecules.
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Affiliation(s)
- L De Benedictis
- Dipartimento di Farmacologia e Fisiologia Umana, Policlinico, Piazza Giulio Cesare, I-70124, Bari, Italy
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9
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Seroussi E, Shani N, Ben-Meir D, Chajut A, Divinski I, Faier S, Gery S, Karby S, Kariv-Inbal Z, Sella O, Smorodinsky NI, Lavi S. Uniquely conserved non-translated regions are involved in generation of the two major transcripts of protein phosphatase 2Cbeta. J Mol Biol 2001; 312:439-51. [PMID: 11563908 DOI: 10.1006/jmbi.2001.4967] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Partial cDNAs of different isoforms of protein phosphatase 2Cbeta (PP2Cbeta or PPM1B) have been characterized in mammals. We disclose here the full cDNAs of two major PP2Cbeta isoforms from human, rat and mouse. These cDNAs (2.6 and 3.3 kb) are able to encode 53 kDa (PP2Cbetal) and 43 kDa (PP2Cbetas) polypeptides, respectively. The isoforms are co-expressed ubiquitously with the highest level in skeletal muscle, as assessed by Northern-blot analysis. Western and in situ analyses using monoclonal antibodies against PP2Cbeta confirmed the existence of two isoforms in the cytoplasm. Comparative sequence analysis revealed that both cDNAs consist of six exons with an alternate usage of the 3' exons that underlies the differences between them. The genomic structure of PP2Cbeta is similar to that of other PP2C paralogs and includes a non-coding first exon followed by a large intron and a large second exon that encoded most of the catalytic domain. Both variants of the ending exon include large non-coding regions. All non-translated regions (NTRs) are highly conserved between the orthologous genes, indicating their regulatory function. The 5'-NTR is long (379 bp), includes upstream start codons and is predicted to contain stable secondary structures. Such features inhibit translation initiation by the scanning mechanism. Introduction of this NTR element into a bi-luciferase expression-cassette enabled expression of the second cistron, suggesting that it might serve as an internal ribosome entry site, or it contains a cryptic promoter. Overexpression of PP2Cbeta under CMV-promoter in 293 cells led to cell-growth arrest or cell death.
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Affiliation(s)
- E Seroussi
- Institute of Animal Science, Volcani Center, Bet-Dagan, 50250, Israel
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Machida H, Ito M, Okamoto R, Shiraki K, Isaka N, Hartshorne DJ, Nakano T. Molecular cloning and analysis of the 5'-flanking region of the human MYPT1 gene. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1517:424-9. [PMID: 11342221 DOI: 10.1016/s0167-4781(00)00285-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have cloned and sequenced a 5 kb genomic fragment in the 5'-flanking region of the human myosin phosphatase target subunit 1. The transcription initiation site (+1) was 268 bp upstream from the translation start site. In this promoter there are no canonical TATA or CAAT box elements but there is a high GC-rich sequence. Basal promoter activity was due to the GC-rich region that contained one Sp1 transcription factor binding site, thus demonstrating that the MYPT1 gene is a housekeeping gene. Luciferase reporter assays showed the presence of two regions for positive elements and one for a negative element.
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Affiliation(s)
- H Machida
- First Department of Internal Medicine, University School of Medicine, Tsu, Mie, Japan
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Fear MW, Kelsell DP, Spurr NK, Barnes MR. Wnt-16a, a novel Wnt-16 isoform, which shows differential expression in adult human tissues. Biochem Biophys Res Commun 2000; 278:814-20. [PMID: 11095990 DOI: 10.1006/bbrc.2000.3852] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The WNT genes encode a large family of secreted glycoprotein signalling molecules important from the earliest stages of development through to the adult. We have identified a novel isoform of the recently described WNT family member, Wnt16, following analysis of chromosome 7q31 genomic sequence. We find differential organisation of Wnt16 with the generation of two mRNA isoforms, Wnt16a and Wnt16b. These isoforms differ in the composition of their 5'-UTR and first exons and show evidence of differential expression. In normal human tissues, Wnt16a is expressed at significant levels only in the pancreas, whereas Wnt16b is expressed more ubiquitously with highest levels in adult kidney, placenta, brain, heart, and spleen. Wnt16 is one of a growing number of WNT genes showing evidence of distinct isoforms. We present evidence to suggest that these isoforms may be regulated from alternative promoters and discuss the potential functional differentiation afforded by these WNT isoforms. This may reveal subtle new mechanisms of regulation of WNT expression and function.
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Affiliation(s)
- M W Fear
- Centre for Cutaneous Research, St. Bartholomew's and the Royal London Hospital School of Medicine and Dentistry, 2 Newark Street, London, E1 2AT, United Kingdom
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