1
|
Schniers A, Goll R, Pasing Y, Sørbye SW, Florholmen J, Hansen T. Ulcerative colitis: functional analysis of the in-depth proteome. Clin Proteomics 2019; 16:4. [PMID: 30718987 PMCID: PMC6350310 DOI: 10.1186/s12014-019-9224-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 01/22/2019] [Indexed: 12/19/2022] Open
Abstract
Background Ulcerative colitis (UC) is one major form of inflammatory bowel disease. The cause and the pathophysiology of the disease are not fully understood and we therefor aim in this study to identify important pathophysiological features in UC from proteomics data. Methods Colon mucosa biopsies from inflamed tissue of untreated UC patients at diagnosis and from healthy controls were obtained during colonoscopy. Quantitative protein data was acquired by bottom-up proteomics and furthermore processed with MaxQuant. The quantitative proteome data was analyzed with Perseus and enrichment data was analyzed by ClueGO for Cytoscape. Results The generated proteome dataset is to-date the deepest from colon mucosa biopsies with 8562 identified proteins whereof 6818 were quantified in > 70% of the samples. We report abundance differences between UC and healthy controls and the respective p values for all quantified proteins in the supporting information. From this data set enrichment analysis revealed decreased protein abundances in UC for metallothioneins, PPAR-inducible proteins, fibrillar collagens and proteins involved in bile acid transport as well as metabolic functions of nutrients, energy, steroids, xenobiotics and carbonate. On the other hand increased abundances were enriched in immune response and protein processing in the endoplasmic reticulum, e.g. unfolded protein response and signal peptidase complex proteins. Conclusions This explorative study describes the most affected functions in UC tissue. Our results complemented previous findings substantially. Decreased abundances of signal peptidase complex proteins in UC are a new discovery. Electronic supplementary material The online version of this article (10.1186/s12014-019-9224-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Armin Schniers
- 1Natural Products and Medicinal Chemistry Research Group, Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Rasmus Goll
- 2Department of Medical Gastroenterology, University Hospital of North Norway, Tromsø, Norway.,3Gastroenterology and Nutrition Research Group, Department of Clinical Medicine, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Yvonne Pasing
- 4Division of Internal Medicine, University Hospital of North Norway, Tromsø, Norway
| | | | - Jon Florholmen
- 2Department of Medical Gastroenterology, University Hospital of North Norway, Tromsø, Norway.,3Gastroenterology and Nutrition Research Group, Department of Clinical Medicine, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Terkel Hansen
- 1Natural Products and Medicinal Chemistry Research Group, Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| |
Collapse
|
2
|
Hua L, Yong C, Zhanquan Z, Boqiang L, Guozheng Q, Shiping T. Pathogenic mechanisms and control strategies of Botrytis cinerea causing post-harvest decay in fruits and vegetables. FOOD QUALITY AND SAFETY 2018. [DOI: 10.1093/fqsafe/fyy016] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Li Hua
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing
- University of Chinese Academy of Sciences, Beijing
| | - Chen Yong
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing
- University of Chinese Academy of Sciences, Beijing
| | - Zhang Zhanquan
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing
- Key Laboratory of Post-Harvest Handing of Fruits, Ministry of Agriculture of China, Institute of Botany, Chinese Academy of Sciences, China
| | - Li Boqiang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing
- Key Laboratory of Post-Harvest Handing of Fruits, Ministry of Agriculture of China, Institute of Botany, Chinese Academy of Sciences, China
| | - Qin Guozheng
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing
- Key Laboratory of Post-Harvest Handing of Fruits, Ministry of Agriculture of China, Institute of Botany, Chinese Academy of Sciences, China
| | - Tian Shiping
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing
- University of Chinese Academy of Sciences, Beijing
- Key Laboratory of Post-Harvest Handing of Fruits, Ministry of Agriculture of China, Institute of Botany, Chinese Academy of Sciences, China
| |
Collapse
|
3
|
Zucchelli S, Patrucco L, Persichetti F, Gustincich S, Cotella D. Engineering Translation in Mammalian Cell Factories to Increase Protein Yield: The Unexpected Use of Long Non-Coding SINEUP RNAs. Comput Struct Biotechnol J 2016; 14:404-410. [PMID: 27872686 PMCID: PMC5107644 DOI: 10.1016/j.csbj.2016.10.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/21/2016] [Accepted: 10/24/2016] [Indexed: 12/26/2022] Open
Abstract
Mammalian cells are an indispensable tool for the production of recombinant proteins in contexts where function depends on post-translational modifications. Among them, Chinese Hamster Ovary (CHO) cells are the primary factories for the production of therapeutic proteins, including monoclonal antibodies (MAbs). To improve expression and stability, several methodologies have been adopted, including methods based on media formulation, selective pressure and cell- or vector engineering. This review presents current approaches aimed at improving mammalian cell factories that are based on the enhancement of translation. Among well-established techniques (codon optimization and improvement of mRNA secondary structure), we describe SINEUPs, a family of antisense long non-coding RNAs that are able to increase translation of partially overlapping protein-coding mRNAs. By exploiting their modular structure, SINEUP molecules can be designed to target virtually any mRNA of interest, and thus to increase the production of secreted proteins. Thus, synthetic SINEUPs represent a new versatile tool to improve the production of secreted proteins in biomanufacturing processes.
Collapse
Affiliation(s)
- Silvia Zucchelli
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy; Area of Neuroscience, SISSA, Trieste, Italy
| | - Laura Patrucco
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | | | - Stefano Gustincich
- Area of Neuroscience, SISSA, Trieste, Italy; Department of Neuroscience and Brain Technologies, Italian Institute of Technology (IIT), Genova, Italy
| | - Diego Cotella
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| |
Collapse
|
4
|
Kida Y, Ishihara Y, Fujita H, Onishi Y, Sakaguchi M. Stability and flexibility of marginally hydrophobic-segment stalling at the endoplasmic reticulum translocon. Mol Biol Cell 2016; 27:930-40. [PMID: 26823014 PMCID: PMC4791137 DOI: 10.1091/mbc.e15-09-0672] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/19/2016] [Indexed: 01/10/2023] Open
Abstract
Many membrane proteins are integrated into the endoplasmic reticulum membrane through the protein-conducting channel, the translocon. Transmembrane segments with insufficient hydrophobicity for membrane integration are frequently found in multispanning membrane proteins, and such marginally hydrophobic (mH) segments should be accommodated, at least transiently, at the membrane. Here we investigated how mH-segments stall at the membrane and their stability. Our findings show that mH-segments can be retained at the membrane without moving into the lipid phase and that such segments flank Sec61α, the core channel of the translocon, in the translational intermediate state. The mH-segments are gradually transferred from the Sec61 channel to the lipid environment in a hydrophobicity-dependent manner, and this lateral movement may be affected by the ribosome. In addition, stalling mH-segments allow for insertion of the following transmembrane segment, forming an Ncytosol/Clumen orientation, suggesting that mH-segments can move laterally to accommodate the next transmembrane segment. These findings suggest that mH-segments may be accommodated at the ER membrane with lateral fluctuation between the Sec61 channel and the lipid phase.
Collapse
Affiliation(s)
- Yuichiro Kida
- Graduate School of Life Science, University of Hyogo, Kamigori, Hyogo 678-1297, Japan
| | - Yudai Ishihara
- Graduate School of Life Science, University of Hyogo, Kamigori, Hyogo 678-1297, Japan
| | - Hidenobu Fujita
- Graduate School of Life Science, University of Hyogo, Kamigori, Hyogo 678-1297, Japan
| | - Yukiko Onishi
- Graduate School of Life Science, University of Hyogo, Kamigori, Hyogo 678-1297, Japan
| | - Masao Sakaguchi
- Graduate School of Life Science, University of Hyogo, Kamigori, Hyogo 678-1297, Japan
| |
Collapse
|
5
|
Abstract
Autophagy is a lysosomal degradation process crucial for adaptation to stress and cellular homeostasis. In cancer, autophagy has been demonstrated to serve multifaceted roles in tumor initiation and progression. Although genetic evidence corroborates a role for autophagy as a tumor suppressor mechanism during tumor initiation, autophagy also sustains metabolic pathways in cancer cells and promotes survival within the harsh tumor microenvironment and in response to diverse anticancer therapies. Moreover, though traditionally viewed as an autodigestive process, more recent work demonstrates that autophagy also facilitates cellular secretion; the importance of these new functions of the autophagy pathway is being increasingly appreciated during cancer progression and treatment. In this review, we discuss how these evolving and diverse roles for autophagy both impede and promote tumorigenesis.
Collapse
Affiliation(s)
- J Liu
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, United States
| | - J Debnath
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, United States.
| |
Collapse
|
6
|
Koppel I, Tuvikene J, Lekk I, Timmusk T. Efficient use of a translation start codon in BDNF exon I. J Neurochem 2015; 134:1015-25. [PMID: 25868795 DOI: 10.1111/jnc.13124] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 04/01/2015] [Accepted: 04/02/2015] [Indexed: 12/31/2022]
Abstract
The brain-derived neurotrophic factor (BDNF) gene contains a number of 5' exons alternatively spliced with a common 3' exon. BDNF protein is synthesized from alternative transcripts as a prepro-precursor encoded by the common 3' exon IX, which has a translation start site 21 bp downstream of the splicing site. BDNF mRNAs containing exon I are an exception to this arrangement as the last three nucleotides of this exon constitute an in-frame AUG. Here, we show that this AUG is efficiently used for translation initiation in PC12 cells and cultured cortical neurons. Use of exon I-specific AUG produces higher levels of BDNF protein than use of the common translation start site, resulting from a higher translation rate. No differences in protein degradation, constitutive or regulated secretion were detected between BDNF isoforms with alternative 5' termini. As the BDNF promoter preceding exon I is known to be highly regulated by neuronal activity, our results suggest that the function of this translation start site may be efficient stimulus-dependent synthesis of BDNF protein. The brain-derived neurotrophic factor (BDNF) gene contains multiple untranslated 5' exons alternatively spliced to one common protein-coding 3' exon. However, exon I contains an in-frame ATG in a favorable translation context. Here, we show that use of this ATG is associated with more efficient protein synthesis than the commonly used ATG in exon IX.
Collapse
Affiliation(s)
- Indrek Koppel
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Jürgen Tuvikene
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Ingrid Lekk
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | - Tõnis Timmusk
- Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| |
Collapse
|
7
|
Yamagishi M, Onishi Y, Yoshimura S, Fujita H, Imai K, Kida Y, Sakaguchi M. A few positively charged residues slow movement of a polypeptide chain across the endoplasmic reticulum membrane. Biochemistry 2014; 53:5375-83. [PMID: 25093244 DOI: 10.1021/bi500649y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Many polypeptide chains are translocated across and integrated into the endoplasmic reticulum membrane through protein-conducting channels. During the process, amino acid sequences of translocating polypeptide chains are scanned by the channels and classified to be retained in the membrane or translocated into the lumen. We established an experimental system with which the kinetic effect of each amino acid residue on the polypeptide chain movement can be analyzed with a time resolution of tens of seconds. Positive charges greatly slow movement; only two lysine residues caused a remarkable slow down, and their effects were additive. The lysine residue was more effective than arginine. In contrast, clusters comprising three residues of each of the other 18 amino acids had little effect on chain movement. We also demonstrated that a four lysine cluster can exert the effect after being fully exposed from the ribosome. We concluded that as few as two to three residues of positively charged amino acids can slow the movement of the nascent polypeptide chain across the endoplasmic reticulum membrane. This effect provides a fundamental basis of the topogenic function of positively charged amino acids.
Collapse
Affiliation(s)
- Marifu Yamagishi
- Graduate School of Life Science, University of Hyogo , Kouto Ako-gun, Hyogo 678-1297 Japan
| | | | | | | | | | | | | |
Collapse
|
8
|
|
9
|
Zhang Z, Qin G, Li B, Tian S. Knocking out Bcsas1 in Botrytis cinerea impacts growth, development, and secretion of extracellular proteins, which decreases virulence. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:590-600. [PMID: 24520899 DOI: 10.1094/mpmi-10-13-0314-r] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Pathogenic fungi usually secrete a series of virulence factors to the extracellular environment to facilitate infection. Rab GTPases play a central role in the secretory pathway. To explore the function of Rab/GTPase in filamentous fungi, we knocked out a Rab/GTPase family gene, Bcsas1, in Botrytis cinerea, an aggressive fungal pathogen that infects more than 200 plant species. A detailed analysis was conducted on the virulence and the secretory capability of the mutants. The results indicated that knockout of Bcsas1 inhibited hyphal development and reduced sporulation of B. cinerea on potato dextrose agar plates resulting in reduced virulence on various fruit hosts. Knocking out the Bcsas1 gene led to an accumulation of transport vesicles at the hyphal tip, significantly reduced extracellular protein content, and lowered the activity of polygalacturonase and xylanase in the extracellular medium. However, mutation of Bcsas1 did not affect the expression of genes encoding polygalacturonase and xylanase, suggesting the secretion of these two family enzymes was suppressed in the mutant. Moreover, a comparative analysis of the secretome provided further evidence that the disruption of Bcsas1 in mutant strains significantly depressed the secretion of polysaccharide hydrolases and proteases. The results indicate that Bcsas1, the Rab8/SEC4-like gene, plays a crucial role in development, protein secretion, and virulence of B. cinerea.
Collapse
|
10
|
Wang P, Huang L, Jiang H, Tian J, Chu X, Wu N. Improving the secretion of a methyl parathion hydrolase in Pichia pastoris by modifying its N-terminal sequence. PLoS One 2014; 9:e96974. [PMID: 24806460 PMCID: PMC4013123 DOI: 10.1371/journal.pone.0096974] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 04/14/2014] [Indexed: 11/29/2022] Open
Abstract
Pichia pastoris is commonly used to express and secrete target proteins, although not all recombinant proteins can be successfully produced. In this study, we used methyl parathion hydrolase (MPH) from Ochrobactrum sp. M231 as a model to study the importance of the N-terminus of the protein for its secretion. While MPH can be efficiently expressed intracellularly in P. pastoris, it is not secreted into the extracellular environment. Three MPH mutants (N66-MPH, D10-MPH, and N9-MPH) were constructed through modification of its N-terminus, and the secretion of each by P. pastoris was improved when compared to wild-type MPH. The level of secreted D10-MPH was increased to 0.21 U/mL, while that of N9-MPH was enhanced to 0.16 U/mL. Although N66-MPH was not enzymatically active, it was secreted efficiently, and was identified by SDS-PAGE. These results demonstrate that the secretion of heterologous proteins in P. pastoris may be improved by modifying their N-terminal structures.
Collapse
Affiliation(s)
- Ping Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Lu Huang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Hu Jiang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Jian Tian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
- * E-mail:
| | - Xiaoyu Chu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Ningfeng Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| |
Collapse
|
11
|
Yabuki T, Morimoto F, Kida Y, Sakaguchi M. Membrane translocation of lumenal domains of membrane proteins powered by downstream transmembrane sequences. Mol Biol Cell 2013; 24:3123-32. [PMID: 23924896 PMCID: PMC3784385 DOI: 10.1091/mbc.e13-04-0210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The affinity required for the trapping of translocation of a streptavidin-binding peptide–tagged N-terminal domain of a type I signal anchor sequence is determined. Using the same tagging method, this study also detects the cytosolic stall of lumenal loops of a multispanning membrane protein and the translocation by the following TM sequence. Translocation of the N-terminus of a type I signal anchor (SA-I) sequence across the endoplasmic reticulum membrane can be arrested by tagging with a streptavidin-binding peptide tag (SBP tag) and trapping by streptavidin. In the present study, we first examine the affinity required for the translocation arrest. When the SBP tag is serially truncated, the ability for arrest gradually decreases. Surface plasmon resonance analysis shows that an interaction as strong as 10−8 M or a smaller dissociation constant is required for trapping the topogenesis of a natural SA-I sequence. Such truncated tags, however, become effective by mutating the SA-I sequence, suggesting that the translocation motivation is considerably influenced by the properties of the SA-I sequence. In addition, we introduce the SBP tag into lumenal loops of a multispanning membrane protein, human erythrocyte band 3. Among the tagged loops between transmembrane 1 (TM1) and TM8, three loops are trapped by cytosolic streptavidin. These loops are followed by TM sequences possessing topogenic properties, like the SA-I sequence, and translocation of one loop is diminished by insertion of a proline into the following TM sequence. These findings suggest that the translocation of lumenal loops by SA-I–like TM sequences has a crucial role in topogenesis of multispanning membrane proteins.
Collapse
Affiliation(s)
- Takaaki Yabuki
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako-gun, Hyogo 678-1297, Japan
| | | | | | | |
Collapse
|
12
|
Samuel P, Prasanna Vadhana AK, Kamatchi R, Antony A, Meenakshisundaram S. Effect of molecular chaperones on the expression of Candida antarctica lipase B in Pichia pastoris. Microbiol Res 2013; 168:615-20. [PMID: 23871144 DOI: 10.1016/j.micres.2013.06.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 04/18/2013] [Accepted: 06/18/2013] [Indexed: 10/26/2022]
Abstract
One of the reasons for limited heterologous protein secretion in Pichia pastoris is the suboptimal folding conditions inside the cell. The Hsp70 and Hsp40 chaperone families in the cytoplasm or the ER regulate the folding and secretion of heterologous proteins. Here, we have studied the effect of chaperones Ydj1p, Ssa1p, Sec63p and Kar2p on the secretory expression of Candida antarctica lipase B (CalB) protein. Expression of CalB in P. pastoris resulted in the induction of Kar2p secretion into the medium surpassing the retrieval capacity of the cell. Individual overexpression of Ydj1p, Ssa1p and Sec63p in recombinant P. pastoris increased CalB expression level by 1.6-, 1.4- and 1.4-fold respectively compared to the control strain harboring only the CalB gene. However, overexpression of Kar2p had a negative effect on the expression of CalB. Moreover, Western blot analysis indicated accumulation and secretion of Kar2p in the ER, Golgi and extracellular medium in the chaperone coexpression strains. When expressed in combinations such as Ydj1p-Ssa1p, Ydj1p-Sec63p, Kar2p-Ssa1p, Kar2p-Sec63p, the expression level of CalB was increased by 2.5-, 1.5-, 1.5- and 1.5-fold respectively. Contrastingly, the Kar2p-Ydj1p combination resulted in decreased CalB secretion in the supernatant. From these results, we conclude that overexpression of Kar2p is not required for the secretion of CalB. Also, our work confirmed the synergistic effect of Ssa1p and Ydj1p chaperones in the expression of CalB.
Collapse
Affiliation(s)
- Premsingh Samuel
- Centre for Biotechnology, Anna University, Chennai 600 025, India
| | | | | | | | | |
Collapse
|
13
|
Control of IgG LC:HC ratio in stably transfected CHO cells and study of the impact on expression, aggregation, glycosylation and conformational stability. J Biotechnol 2013; 165:157-66. [DOI: 10.1016/j.jbiotec.2013.03.019] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 03/28/2013] [Accepted: 03/28/2013] [Indexed: 11/22/2022]
|
14
|
Phosphatidylserine-binding protein lactadherin inhibits protein translocation across the ER membrane. Biochem Biophys Res Commun 2013; 434:620-6. [PMID: 23583395 DOI: 10.1016/j.bbrc.2013.03.131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 03/29/2013] [Indexed: 01/13/2023]
Abstract
Secretory and membrane proteins are translocated across and inserted into the endoplasmic reticulum membrane via translocon channels. To investigate the effect of the negatively-charged phospholipid phosphatidylserine on the translocation of nascent polypeptide chains through the translocon, we used the phosphatidylserine-binding protein lactadherin C2-domain. Lactadherin inhibited targeting of nascent chain to the translocon by signal sequence and the initiation of translocation. Moreover, lactadherin inhibited the movement of the translocating polypeptide chain regardless of the presence or absence of positively-charged residues. Phosphatidylserine might be critically involved in translocon function, but it is not a major determinant for translocation arrest of positively-charged residues.
Collapse
|
15
|
Drugmand JC, Schneider YJ, Agathos SN. Insect cells as factories for biomanufacturing. Biotechnol Adv 2012; 30:1140-57. [DOI: 10.1016/j.biotechadv.2011.09.014] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 09/13/2011] [Accepted: 09/16/2011] [Indexed: 10/17/2022]
|
16
|
Secretory signal peptide modification for optimized antibody-fragment expression-secretion in Leishmania tarentolae. Microb Cell Fact 2012; 11:97. [PMID: 22830363 PMCID: PMC3416730 DOI: 10.1186/1475-2859-11-97] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 07/01/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Secretory signal peptides (SPs) are well-known sequence motifs targeting proteins for translocation across the endoplasmic reticulum membrane. After passing through the secretory pathway, most proteins are secreted to the environment. Here, we describe the modification of an expression vector containing the SP from secreted acid phosphatase 1 (SAP1) of Leishmania mexicana for optimized protein expression-secretion in the eukaryotic parasite Leishmania tarentolae with regard to recombinant antibody fragments. For experimental design the online tool SignalP was used, which predicts the presence and location of SPs and their cleavage sites in polypeptides. To evaluate the signal peptide cleavage site as well as changes of expression, SPs were N-terminally linked to single-chain Fragment variables (scFv's). The ability of L. tarentolae to express complex eukaryotic proteins with highly diverse post-translational modifications and its easy bacteria-like handling, makes the parasite a promising expression system for secretory proteins. RESULTS We generated four vectors with different SP-sequence modifications based on in-silico analyses with SignalP in respect to cleavage probability and location, named pLTEX-2 to pLTEX-5. To evaluate their functionality, we cloned four individual scFv-fragments into the vectors and transfected all 16 constructs into L. tarentolae. Independently from the expressed scFv, pLTEX-5 derived constructs showed the highest expression rate, followed by pLTEX-4 and pLTEX-2, whereas only low amounts of protein could be obtained from pLTEX-3 clones, indicating dysfunction of the SP. Next, we analysed the SP cleavage sites by Edman degradation. For pLTEX-2, -4, and -5 derived scFv's, the results corresponded to in-silico predictions, whereas pLTEX-3 derived scFv's contained one additional amino-acid (AA). CONCLUSIONS The obtained results demonstrate the importance of SP-sequence optimization for efficient expression-secretion of scFv's. We could successfully demonstrate that minor modifications in the AA-sequence in the c-region of the natural SP from SAP1, based on in-silico predictions following the (-3, -1) rule, resulted in different expression-secretion rates of the protein of interest. The yield of scFv production could be improved close to one order of magnitude. Therefore, SP-sequence optimization is a viable option to increase the overall yield of recombinant protein production.
Collapse
|
17
|
Yamamoto H, Fujita H, Kida Y, Sakaguchi M. Pleiotropic effects of membrane cholesterol upon translocation of protein across the endoplasmic reticulum membrane. Biochemistry 2012; 51:3596-605. [PMID: 22493992 DOI: 10.1021/bi2018915] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Various proteins are translocated through and inserted into the endoplasmic reticulum membrane via translocon channels. The hydrophobic segments of signal sequences initiate translocation, and those on translocating polypeptides interrupt translocation to be inserted into the membrane. Positive charges suppress translocation to regulate the orientation of the signal sequences. Here, we investigated the effect of membrane cholesterol on the translocational behavior of nascent chains in a cell-free system. We found that the three distinct translocation processes were sensitive to membrane cholesterol. Cholesterol inhibited the initiation of translocation by the signal sequence, and the extent of inhibition depended on the signal sequence. Even when initiation was not inhibited, cholesterol impeded the movement of the positively charged residues of the translocating polypeptide chain. In surprising contrast, cholesterol enhanced the translocation of hydrophobic sequences through the translocon. On the basis of these findings, we propose that membrane cholesterol greatly affects partitioning of hydrophobic segments into the membrane and impedes the movement of positive charges.
Collapse
Affiliation(s)
- Hitoshi Yamamoto
- Graduate School of Life Science, University of Hyogo, Kouto 3-2-1, Ako-gun, Hyogo 678-1297, Japan
| | | | | | | |
Collapse
|
18
|
Fujita H, Yamagishi M, Kida Y, Sakaguchi M. Positive charges on the translocating polypeptide chain arrest movement through the translocon. J Cell Sci 2012; 124:4184-93. [PMID: 22223880 DOI: 10.1242/jcs.086850] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Polypeptide chains synthesized by membrane-bound ribosomes are translocated through, and integrated into, the endoplasmic reticulum (ER) membrane by means of the protein translocation channel, the translocon. Positive charges on the nascent chain determine the orientation of the hydrophobic segment as it is inserted into the translocon and enhance the stop-translocation of translocating hydrophobic segments. Here we show that positive charges temporarily arrested ongoing polypeptide chain movement through the ER translocon by electrostatic interaction, even in the absence of a hydrophobic segment. The C-terminus of the polypeptide chain was elongated during the arrest, and then the full-length polypeptide chain moved through the translocon. The translocation-arrested polypeptide was not anchored to the membrane and the charges were on the cytoplasmic side of the membrane. The arrest effect was prevented by negatively charged residues inserted into the positive-charge cluster, and it was also suppressed by high salt conditions. We propose that positive charges are independent translocation regulators that are more active than previously believed.
Collapse
Affiliation(s)
- Hidenobu Fujita
- Graduate School of Life Science, University of Hyogo, Kouto Ako-gun, Hyogo 678-1297, Japan
| | | | | | | |
Collapse
|
19
|
Nakamura S, Abe F, Kawahigashi H, Nakazono K, Tagiri A, Matsumoto T, Utsugi S, Ogawa T, Handa H, Ishida H, Mori M, Kawaura K, Ogihara Y, Miura H. A wheat homolog of MOTHER OF FT AND TFL1 acts in the regulation of germination. THE PLANT CELL 2011; 23:3215-29. [PMID: 21896881 PMCID: PMC3203438 DOI: 10.1105/tpc.111.088492] [Citation(s) in RCA: 182] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 08/11/2011] [Accepted: 08/23/2011] [Indexed: 05/18/2023]
Abstract
Seed dormancy is an adaptive mechanism and an important agronomic trait. Temperature during seed development strongly affects seed dormancy in wheat (Triticum aestivum) with lower temperatures producing higher levels of seed dormancy. To identify genes important for seed dormancy, we used a wheat microarray to analyze gene expression in embryos from mature seeds grown at lower and higher temperatures. We found that a wheat homolog of MOTHER OF FT AND TFL1 (MFT) was upregulated after physiological maturity in dormant seeds grown at the lower temperature. In situ hybridization analysis indicated that MFT was exclusively expressed in the scutellum and coleorhiza. Mapping analysis showed that MFT on chromosome 3A (MFT-3A) colocalized with the seed dormancy quantitative trait locus (QTL) QPhs.ocs-3A.1. MFT-3A expression levels in a dormant cultivar used for the detection of the QTL were higher after physiological maturity; this increased expression correlated with a single nucleotide polymorphism in the promoter region. In a complementation analysis, high levels of MFT expression were correlated with a low germination index in T1 seeds. Furthermore, precocious germination of isolated immature embryos was suppressed by transient introduction of MFT driven by the maize (Zea mays) ubiquitin promoter. Taken together, these results suggest that MFT plays an important role in the regulation of germination in wheat.
Collapse
Affiliation(s)
- Shingo Nakamura
- National Institute of Crop Science, Tsukuba 305-8518, Japan
- Address correspondence to
| | - Fumitaka Abe
- National Institute of Crop Science, Tsukuba 305-8518, Japan
| | | | - Kou Nakazono
- National Agricultural Research Center, Tsukuba 305-8666, Japan
| | - Akemi Tagiri
- National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
| | - Takashi Matsumoto
- National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
| | - Shigeko Utsugi
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Taiichi Ogawa
- National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
| | - Hirokazu Handa
- National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Hiroki Ishida
- Department of Crop Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, Japan
| | - Masahiko Mori
- National Institute of Crop Science, Tsukuba 305-8518, Japan
| | - Kanako Kawaura
- Kihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan
| | - Yasunari Ogihara
- Kihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan
| | - Hideho Miura
- Department of Crop Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, Japan
| |
Collapse
|
20
|
Cui S, Wu C, Zhou H, Zhao R, Guo L, Wang J, Hung T. Secretory expression of all 16 subtypes of the hemagglutinin 1 protein of influenza A virus in insect cells. J Virol Methods 2011; 177:160-7. [PMID: 21827791 DOI: 10.1016/j.jviromet.2011.07.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2011] [Revised: 07/19/2011] [Accepted: 07/25/2011] [Indexed: 11/29/2022]
Abstract
Influenza viruses are known for their ability to change their antigenic structure and create new viral strains. Hemagglutinin (HA), for which 16 subtypes have been identified, is a major antigenic determinant essential for the pathogenesis of influenza A viruses. To predict and monitor future epidemics, it is critical to produce various HA subtype antigens conveniently and rapidly. A simple, effective, and economic method to generate subunit HA1 of all 16 HA subtypes as recombinant proteins (rHA1) is reported. rHA1 proteins are expressed in insect cells as secretory proteins after integration into a baculovirus expression vector containing a 6×His tag element and the signal peptide of the GP67 protein, a membrane glycoprotein identified in Autographa californica nuclear polyhedrosis virus. The proteins can be purified to ≥90% purity using a single Ni(2+)-chelating affinity chromatography step, yielding a recovery rate of about 50%. The rHA1 proteins elicit high titer antibodies in mice and show high specificity in Western blots. This study paves the way for subtype specific detection methods and for future studies of the immune relationships among the subtypes of influenza A virus HA proteins.
Collapse
Affiliation(s)
- Shujuan Cui
- State Key Laboratory of Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | | | | | | | | | | | | |
Collapse
|
21
|
Yamagishi M, Fujita H, Morimoto F, Kida Y, Sakaguchi M. A sugar chain at a specific position in the nascent polypeptide chain induces forward movement during translocation through the translocon. J Biochem 2011; 149:591-600. [PMID: 21278156 DOI: 10.1093/jb/mvr011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Nascent polypeptide chains synthesized by membrane bound ribosomes are cotranslationally translocated through and integrated into the endoplasmic reticulum translocon. Hydrophobic segments and positive charges on the chain are critical to halt the ongoing translocation. A marginally hydrophobic segment, which cannot be inserted into the membrane by itself, can be a transmembrane segment depending on its downstream positive charges. In certain conditions, positive charges even 60 residues downstream cause the marginally hydrophobic segment to span the membrane by inducing the segment to slide back from the lumen. Here we systematically examined the effect of a core sugar chain on the fate of a marginally hydrophobic segment using a cell-free translation and translocation system. A sugar chain added within 12 residues upstream of the marginally hydrophobic segment prevents the sliding back and promotes forward movement of the polypeptide chain. The sugar chain apparently functions as a ratchet to keep the polypeptide chain in the lumen. We propose that the sugar chain is a third topology determinant of membrane proteins, in addition to a hydrophobic segment and positive charges of the nascent chain.
Collapse
Affiliation(s)
- Marifu Yamagishi
- Graduate School of Life Science, University of Hyogo, Kouto Ako-gun, Hyogo 678-1297, Japan
| | | | | | | | | |
Collapse
|
22
|
Li Z, Leung W, Yon A, Nguyen J, Perez VC, Vu J, Giang W, Luong LT, Phan T, Salazar KA, Gomez SR, Au C, Xiang F, Thomas DW, Franz AH, Lin-Cereghino J, Lin-Cereghino GP. Secretion and proteolysis of heterologous proteins fused to the Escherichia coli maltose binding protein in Pichia pastoris. Protein Expr Purif 2010; 72:113-24. [PMID: 20230898 PMCID: PMC2860017 DOI: 10.1016/j.pep.2010.03.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2010] [Revised: 03/09/2010] [Accepted: 03/10/2010] [Indexed: 11/19/2022]
Abstract
The Escherichia coli maltose binding protein (MBP) has been utilized as a translational fusion partner to improve the expression of foreign proteins made in E. coli. When located N-terminal to its cargo protein, MBP increases the solubility of intracellular proteins and improves the export of secreted proteins in bacterial systems. We initially explored whether MBP would have the same effect in the methylotrophic yeast Pichia pastoris, a popular eukaryotic host for heterologous protein expression. When MBP was fused as an N-terminal partner to several C-terminal cargo proteins expressed in this yeast, proteolysis occurred between the two peptides, and MBP reached the extracellular region unattached to its cargo. However, in two of three instances, the cargo protein reached the extracellular region as well, and its initial attachment to MBP enhanced its secretion from the cell. Extensive mutagenesis of the spacer region between MBP and its C-terminal cargo protein could not inhibit the cleavage although it did cause changes in the protease target sites in the fusion proteins, as determined by mass spectrometry. Taken together, these results suggested that an uncharacterized P. pastoris protease attacked at different locations in the region C-terminal of the MBP domain, including the spacer and cargo regions, but the MBP domain could still act to enhance the secretion of certain cargo proteins.
Collapse
Affiliation(s)
- Zhiguo Li
- Department of Chemistry, University of the Pacific, Stockton, California 95211
| | - Wilson Leung
- Department of Biological Sciences, University of the Pacific, Stockton, California 95211
| | - Amy Yon
- Department of Biological Sciences, University of the Pacific, Stockton, California 95211
| | - John Nguyen
- Department of Biological Sciences, University of the Pacific, Stockton, California 95211
| | - Vincent C. Perez
- Department of Biological Sciences, University of the Pacific, Stockton, California 95211
| | - Jane Vu
- Department of Biological Sciences, University of the Pacific, Stockton, California 95211
| | - William Giang
- Department of Biological Sciences, University of the Pacific, Stockton, California 95211
| | - Linda T. Luong
- Department of Biological Sciences, University of the Pacific, Stockton, California 95211
| | - Tracy Phan
- Department of Biological Sciences, University of the Pacific, Stockton, California 95211
| | - Katherine A. Salazar
- Department of Biological Sciences, University of the Pacific, Stockton, California 95211
| | - Seth R. Gomez
- Department of Biological Sciences, University of the Pacific, Stockton, California 95211
| | - Colin Au
- Department of Biological Sciences, University of the Pacific, Stockton, California 95211
| | - Fan Xiang
- Shimadzu Biotech Corporation, 7060 Koll Center Parkway, Suite 328, Pleasanton, California 94566
| | - David W. Thomas
- Department of Physiology and Pharmacology, Thomas J. Long School of Pharmacy and Health Sciences, University of the Pacific, Stockton, CA 95211
| | - Andreas H. Franz
- Department of Chemistry, University of the Pacific, Stockton, California 95211
| | - Joan Lin-Cereghino
- Department of Biological Sciences, University of the Pacific, Stockton, California 95211
| | - Geoff P. Lin-Cereghino
- Department of Biological Sciences, University of the Pacific, Stockton, California 95211
| |
Collapse
|
23
|
Ben-Shahar Y, Lu B, Collier DM, Snyder PM, Schnizler M, Welsh MJ. The Drosophila gene CheB42a is a novel modifier of Deg/ENaC channel function. PLoS One 2010; 5:e9395. [PMID: 20195381 PMCID: PMC2827562 DOI: 10.1371/journal.pone.0009395] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Accepted: 02/04/2010] [Indexed: 11/18/2022] Open
Abstract
Degenerin/epithelial Na+ channels (DEG/ENaC) represent a diverse family of voltage-insensitive cation channels whose functions include Na+ transport across epithelia, mechanosensation, nociception, salt sensing, modification of neurotransmission, and detecting the neurotransmitter FMRFamide. We previously showed that the Drosophila melanogaster Deg/ENaC gene lounge lizard (llz) is co-transcribed in an operon-like locus with another gene of unknown function, CheB42a. Because operons often encode proteins in the same biochemical or physiological pathway, we hypothesized that CHEB42A and LLZ might function together. Consistent with this hypothesis, we found both genes expressed in cells previously implicated in sensory functions during male courtship. Furthermore, when coexpressed, LLZ coprecipitated with CHEB42A, suggesting that the two proteins form a complex. Although LLZ expressed either alone or with CHEB42A did not generate ion channel currents, CHEB42A increased current amplitude of another DEG/ENaC protein whose ligand (protons) is known, acid-sensing ion channel 1a (ASIC1a). We also found that CHEB42A was cleaved to generate a secreted protein, suggesting that CHEB42A may play an important role in the extracellular space. These data suggest that CHEB42A is a modulatory subunit for sensory-related Deg/ENaC signaling. These results are consistent with operon-like transcription of CheB42a and llz and explain the similar contributions of these genes to courtship behavior.
Collapse
Affiliation(s)
- Yehuda Ben-Shahar
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Beika Lu
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Daniel M. Collier
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- Department of Molecular Physiology and Biophysics, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Peter M. Snyder
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- Department of Molecular Physiology and Biophysics, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Mikael Schnizler
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Michael J. Welsh
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- Department of Molecular Physiology and Biophysics, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
| |
Collapse
|
24
|
Kida Y, Kume C, Hirano M, Sakaguchi M. Environmental transition of signal-anchor sequences during membrane insertion via the endoplasmic reticulum translocon. Mol Biol Cell 2009; 21:418-29. [PMID: 19955210 PMCID: PMC2814787 DOI: 10.1091/mbc.e09-08-0738] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
We determined the environments of polypeptide chains during membrane translocation and integration using site-directed Cys alkylation. Migration of a signal-anchor sequence into the membrane synchronizes with formation of its TM orientation, and the ER translocon can provide the aqueous pathway capable of two hydrophilic chains. In biogenesis of membrane proteins on the endoplasmic reticulum, a protein-conducting channel called the translocon functions in both the membrane translocation of lumenal domains and the integration of transmembrane segments. Here we analyzed the environments of polypeptide chains during the processes by water-dependent alkylation of N-ethylmaleimide at site-directed Cys residues. Using the technique, the region embedded in the hydrophobic portion of the membrane within a signal-anchor sequence and its shortening by insertion of a Pro residue could be detected. When translocation of the N-terminal domain of the signal-anchor was arrested by trapping an N-terminally fused affinity tag sequence, the signal-anchor was susceptible to alkylation, indicating that its migration into the hydrophobic environment was also arrested. Furthermore, when the tag sequence was separated from the signal-anchor by insertion of a hydrophilic sequence, the signal-anchor became inaccessible to alkylation even in the N-terminally trapped state. This suggests that membrane integration of the signal-anchor synchronizes with partial translocation of its N-terminal domain. Additionally, in an integration intermediate of a membrane protein, both of the two translocation-arrested hydrophilic chains were in an aqueous environment flanking the translocon, suggesting that the translocon provides the hydrophilic pathway capable of at least two translocating chains.
Collapse
Affiliation(s)
- Yuichiro Kida
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan.
| | | | | | | |
Collapse
|
25
|
Moran Y, Weinberger H, Lazarus N, Gur M, Kahn R, Gordon D, Gurevitz M. Fusion and retrotransposition events in the evolution of the sea anemone Anemonia viridis neurotoxin genes. J Mol Evol 2009; 69:115-24. [PMID: 19609479 DOI: 10.1007/s00239-009-9258-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Revised: 06/03/2009] [Accepted: 06/10/2009] [Indexed: 12/01/2022]
Abstract
Sea anemones are sessile predators that use a variety of toxins to paralyze prey and foe. Among these toxins, Types I, II and III are short peptides that affect voltage-gated sodium channels. Anemonia viridis is the only sea anemone species that produces both Types I and III neurotoxin. Although the two toxin types are unrelated in sequence and three-dimensional structure, cloning and comparative analysis of their loci revealed a highly similar sequence at the 5' region, which encodes a signal peptide. This similarity was likely generated by gene fusion and could be advantageous in transcript stability and intracellular trafficking and secretion. In addition, these analyses identified the processed pseudogenes of the two gene families in the genome of A. viridis, probably resulting from retrotransposition events. As presence of processed pseudogenes in the genome requires transcription in germ-line cells, we analyzed oocyte-rich ovaries and found that indeed they contain Types I and III transcripts. This result raises questions regarding the role of toxin transcripts in these tissues. Overall, the retrotransposition and gene fusion events suggest that the genes of both Types I and III neurotoxins evolved in a similar fashion and share a partial common ancestry.
Collapse
Affiliation(s)
- Yehu Moran
- Department of Plant Sciences, Tel-Aviv University, Ramat-Aviv, Israel.
| | | | | | | | | | | | | |
Collapse
|
26
|
Ikeda M, Kida Y, Ikushiro SI, Sakaguchi M. Manipulation of Membrane Protein Topology on the Endoplasmic Reticulum by a Specific Ligand in Living Cells. ACTA ACUST UNITED AC 2005; 138:631-7. [PMID: 16272575 DOI: 10.1093/jb/mvi157] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Almost all integral membrane proteins in the secretory pathway are cotranslationally inserted into the endoplasmic reticulum membrane. Their membrane topology is determined by their amino acid sequences. Here we show that the topology can be manipulated by a factor other than the amino acid sequence. A dihydrofolate reductase (DHFR) domain was fused to the N-terminus of the type I signal-anchor sequence of synaptotagmin II, which mediates translocation of the preceding portion. The DHFR domain was translocated through the membrane in COS7 cells and a transmembrane (TM) topology was achieved. When a DHFR ligand, methotrexate, was added to the culture medium, translocation of the DHFR domain was suppressed and both ends of the signal-anchor sequence remained on the cytoplasmic side. In contrast, translocation of the DHFR domain fused after the signal peptide, which translocates the following region, was not affected by the ligand. The topology-altered fusion protein was anchored to the membrane in a high salt-resistant state, and partially extracted from the membrane under alkali conditions. We concluded that the topology of membrane proteins can be manipulated by a trans-acting factor, even in living cells.
Collapse
Affiliation(s)
- Motoyasu Ikeda
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297
| | | | | | | |
Collapse
|
27
|
Sato Y, Sakaguchi M. Topogenic Properties of Transmembrane Segments of Arabidopsis thaliana NHX1 Reveal a Common Topology Model of the Na+/H+ Exchanger Family. ACTA ACUST UNITED AC 2005; 138:425-31. [PMID: 16272136 DOI: 10.1093/jb/mvi132] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The membrane topology of the Arabidopsis thaliana Na(+)/H(+) exchanger isoform 1 (AtNHX1) was investigated by examining the topogenic function of transmembrane (TM) segments using a cell-free system. Even though the signal peptide found in the human Na(+)/H(+) exchanger (NHE) family is missing, the N-terminal hydrophobic segment was efficiently inserted into the membrane and had an N-terminus lumen topology depending on the next TM segment. The two N-terminal TM segments had the same topology as those of TM2 and TM3 of human NHE1. In contrast, TM2 and TM3 of human NHE1 did not acquire the correct topology when the signal peptide (denoted as TM1) was deleted. Furthermore, there were three hydrophobic segments with the same topogenic properties as the TM9-H10-TM10 segments of human NHE1, which has one lumenal loop (H10) and two flanking TM segments (TM9 and TM10). These data indicate that the plant NHX isoforms can form the common membrane topology proposed for the human NHE family, even though it does not have a signal peptide.
Collapse
Affiliation(s)
- Yoko Sato
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan
| | | |
Collapse
|
28
|
Chen Y, Zhang Y, Yin Y, Gao G, Li S, Jiang Y, Gu X, Luo J. SPD--a web-based secreted protein database. Nucleic Acids Res 2005; 33:D169-73. [PMID: 15608170 PMCID: PMC540047 DOI: 10.1093/nar/gki093] [Citation(s) in RCA: 147] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
With the improved secreted protein prediction approach and comprehensive data sources, including Swiss-Prot, TrEMBL, RefSeq, Ensembl and CBI-Gene, we have constructed secretomes of human, mouse and rat, with a total of 18 152 secreted proteins. All the entries are ranked according to the prediction confidence. They were further annotated via a proteome annotation pipeline that we developed. We also set up a secreted protein classification pipeline and classified our predicted secreted proteins into different functional categories. To make the dataset more convincing and comprehensive, nine reference datasets are also integrated, such as the secreted proteins from the Gene Ontology Annotation (GOA) system at the European Bioinformatics Institute, and the vertebrate secreted proteins from Swiss-Prot. All these entries were grouped via a TribeMCL based clustering pipeline. We have constructed a web-based secreted protein database, which has been publicly available at http://spd.cbi.pku.edu.cn. Users can browse the database via a GO assignment or chromosomal-location-based interface. Moreover, text query and sequence similarity search are also provided, and the sequence and annotation data can be downloaded freely from the SPD website.
Collapse
Affiliation(s)
- Yunjia Chen
- Centre of Bioinformatics, College of Life Sciences, National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing 100871, China
| | | | | | | | | | | | | | | |
Collapse
|
29
|
Meads MB, Medveczky PG. Kaposi's Sarcoma-associated Herpesvirus-encoded Viral Interleukin-6 Is Secreted and Modified Differently Than Human Interleukin-6. J Biol Chem 2004; 279:51793-803. [PMID: 15258150 DOI: 10.1074/jbc.m407382200] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Viral interleukin-6 (vIL-6) is a homolog of cellular IL-6 that is encoded by the Kaposi's sarcoma-associated herpesvirus (KSHV) genome. vIL-6 binds to the IL-6 signal transducer gp130 without the cooperation of the IL-6 high affinity receptor to induce STAT3 DNA binding and cell proliferation. Although vIL-6 is believed to be important in the pathogenesis of KSHV-induced diseases, its secretion and post-translational modifications have not previously been characterized. Pulse-chase analysis revealed that the half-time of vIL-6 secretion is approximately 8-fold longer than that of human IL-6. Yet, the vIL-6 signal sequence targets human IL-6 secretion to nearly wild-type levels. Surprisingly, vIL-6 was not secreted from a cell line that does not express gp130 but expression of human gp130 in these cells enabled the secretion of vIL-6. Consistent with this observation, complete maturation of gp130 N-glycans is inhibited by vIL-6 coexpression, suggesting that the binding of the receptor to vIL-6 occurs intracellularly in early or pre-Golgi compartments. Furthermore, a vIL-6 mutant containing an endoplasmic reticulum retention signal is not secreted but does still induce receptor activation and signaling. Secreted vIL-6 is completely glycosylated at both possible N-glycosylaton sites and contains a large proportion of immature high-mannose glycans that is not typical of cytokines. These findings suggest that vIL-6 may induce gp130 signaling by an exclusively autocrine mechanism that relies on intracellular binding to its receptor. During KSHV infection, vIL-6 may only induce signaling in KSHV-infected cells to benefit the viral life cycle and promote oncogenic transformation.
Collapse
|
30
|
Sato Y, Ariyoshi N, Mihara K, Sakaguchi M. Topogenesis of NHE1: direct insertion of the membrane loop and sequestration of cryptic glycosylation and processing sites just after TM9. Biochem Biophys Res Commun 2004; 324:281-7. [PMID: 15465015 DOI: 10.1016/j.bbrc.2004.09.054] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2004] [Indexed: 10/26/2022]
Abstract
Multispanning membrane proteins are synthesized by membrane-bound ribosomes and integrated into the endoplasmic reticulum membrane cotranslationally. To uncover the topogenic process of membrane loop, of which both ends are in the same side of the membrane, we examined topogenesis of a relatively hydrophobic lumenal loop segment (H10 segment) between TM9 and TM10 of human Na(+)/H(+) exchanger isoform 1 using an in vitro expression system. The H10 segment was translocated through the membrane. Any potential sites created within the H10 segment were not glycosylated. Just after TM9, there are potential glycosylation and signal peptidase processing sites. When the reporter domain of prolactin was fused at the position preceding the H10 segment, these sites were modified by the enzymes, while they were not modified in the original molecule. Thus, we concluded that the H10 segment was translocated through the membrane and directly inserted into the membrane and that its membrane insertion caused sequestration of the preceding processing and glycosylation sites from the lumenal modifying enzymes. This topogenic process shows clear contrast to that of pore loops of K(+) channels, which are once exposed in the lumen and accessible to glycosylation enzyme.
Collapse
Affiliation(s)
- Yoko Sato
- Graduate School of Life Science, University of Hyogo, Ako, Hyogo 678-1297, Japan
| | | | | | | |
Collapse
|
31
|
Umigai N, Sato Y, Mizutani A, Utsumi T, Sakaguchi M, Uozumi N. Topogenesis of two transmembrane type K+ channels, Kir 2.1 and KcsA. J Biol Chem 2003; 278:40373-84. [PMID: 12885768 DOI: 10.1074/jbc.m307451200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Potassium channels, which control the passage of K+ across cell membranes, have two transmembrane segments, M1 and M2, separated by a hydrophobic P region containing a highly conserved signature sequence. Here we analyzed the membrane topogenesis characteristics of the M1, M2, and P regions in two animal and bacterial two-transmembrane segment-type K+ channels, Kir 2.1 and KcsA, using an in vitro translation and translocation system. In contrast to the equivalent transmembrane segment, S5, in the voltage-dependent K+ channel, KAT1, the M1 segment in KcsA, was found to have a strong type II signal-anchor function, which favors the Ncyt/Cexo topology. The N-terminal cytoplasmic region was required for efficient, correctly orientated integration of M1 in Kir 2.1. Analysis of N-terminal modification by in vitro metabolic labeling showed that the N terminus in Kir 2.1 was acetylated. The hydrophobic P region showed no topogenic function, allowing it to form a loop, but not a transmembrane structure in the membrane; this region was transiently exposed in the endoplasmic reticulum lumen during the membrane integration process. M2 was found to possess a stop-transfer function and a type I signal-anchor function, enabling it to span the membrane. The C-terminal cytoplasmic region in KcsA was found to affect the efficiency with which the M2 achieved their final structure. Comparative topogenesis studies of Kir 2.1 and KcsA allowed quantification of the relative contributions of each segment and the cytoplasmic regions to the membrane topology of these two proteins. The membrane topogenesis of the pore-forming structure is discussed using results for Kir 2.1, KcsA, and KAT1.
Collapse
Affiliation(s)
- Naofumi Umigai
- Graduate School of Bioagricultural Sciences, Nagoya University, Japan
| | | | | | | | | | | |
Collapse
|
32
|
Abstract
The achievement of robust and regulated protein production in mammalian cells is a complex process that requires careful consideration of many factors, including transcriptional and translational control elements, RNA processing, gene copy number, mRNA stability, the chromosomal site of gene integration, potential toxicity of recombinant proteins to the host cell, and the genetic properties of the host. Gene transfer into mammalian cells may be effected either by infection with virus that carries the recombinant gene of interest, or by direct transfer of plasmid DNA. This chapter discusses the molecular architecture of non-viral vectors for high-level protein production. Virus-based vectors for gene therapy, protein production, vaccine development and other applications are summarized in a table and described.
Collapse
|
33
|
Taft RA, Denegre JM, Pendola FL, Eppig JJ. Identification of genes encoding mouse oocyte secretory and transmembrane proteins by a signal sequence trap. Biol Reprod 2002; 67:953-60. [PMID: 12193407 DOI: 10.1095/biolreprod.102.005546] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The oocyte plays a key role in follicular development. At all stages of follicular development, oocytes interact with surrounding granulosa cells and promote their differentiation into the types of cells that support further oocyte growth and developmental competence. These interactions suggest the existence of an oocyte-granulosa cell regulatory loop that includes both secreted proteins and cell surface receptors on both cell types. Factors involved in the regulatory loop will therefore contain a signal sequence, which can be used to identify them through a signal sequence trap (SST). A screen of an oocyte SST library identified three classes of oocyte-expressed sequences: known mouse genes, sequences homologous to known mammalian genes, and novel sequences of unknown function. Many of the recovered genes may have roles in the oocyte-granulosa cell regulatory loop. For several of the known mouse genes, new roles in follicular development are implied by identification of their expression, for the first time, in the oocyte. The future characterization of novel sequences may lead to the identification of novel proteins participating in the regulatory loop.
Collapse
|
34
|
Hoque AT, Yamano S, Baccaglini L, Baum BJ. Using salivary glands as a tissue target for gene therapeutics. J Drug Target 2002; 9:485-94. [PMID: 11822820 DOI: 10.3109/10611860108998782] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Gene transfer offers a potential way to correct local and systemic protein deficiency disorders by using genes as drugs, so called gene therapeutics. Salivary glands present an interesting target site for gene therapeutic applications. Herein, we review proofs of concept achieved for salivary glands with in vivo animal models. In that context we discuss problems (general and salivary tissue-specific) that limit immediate clinical use for this application of gene transfer. Ongoing efforts, however, suggest that salivary glands may be suitable as gene therapeutic target sites for drug delivery in the near future.
Collapse
Affiliation(s)
- A T Hoque
- Gene Therapy and Therapeutics Branch, National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD 20892-1190, USA
| | | | | | | |
Collapse
|
35
|
Sato Y, Sakaguchi M, Goshima S, Nakamura T, Uozumi N. Integration of Shaker-type K+ channel, KAT1, into the endoplasmic reticulum membrane: synergistic insertion of voltage-sensing segments, S3-S4, and independent insertion of pore-forming segments, S5-P-S6. Proc Natl Acad Sci U S A 2002; 99:60-5. [PMID: 11756658 PMCID: PMC117514 DOI: 10.1073/pnas.012399799] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
KAT1 is a member of the Shaker family of voltage-dependent K(+) channels, which has six transmembrane segments (called S1-S6), including an amphipathic S4 with several positively charged residues and a hydrophobic pore-forming region (called P) between S5 and S6. In this study, we systematically evaluated the function of individual and combined transmembrane segments of KAT1 to direct the final topology in the endoplasmic reticulum membrane by in vitro translation and translocation experiments. The assay with single-transmembrane constructs showed that S1 possesses the type II signal-anchor function, whereas S2 has the stop-transfer function. The properties fit well with the results derived from combined insertion of S1 and S2. S3 and S4 failed to integrate into the membrane by themselves. The inserted glycosylation sequence at the S3-S4 loop neither prevented the translocation of S3 and S4 nor impaired the function of voltage-dependent K(+) transport regardless of the changed length of the S3-S4 loop. S3 and S4 are likely to be posttranslationally integrated into the membrane only when somewhat specific interaction occurs between them. S5 had the ability of translocation reinitiation, and S6 had a strong preference for N(exo)/C(cyt) orientation. The pore region resided outside because of its lack of its transmembrane-spanning property. According to their own topogenic function, combined constructs of S5-P-S6 conferred the membrane-pore-membrane topology. This finding supports the notion that a set of S5-P-S6 can be independently integrated into the membrane. The results in this study provide the fundamental topogenesis mechanism of transmembrane segments involving voltage sensor and pore region in KAT1.
Collapse
Affiliation(s)
- Yoko Sato
- Graduate School of Bioagricultural Sciences, and Bioscience Center, Nagoya University, Nagoya 464-8601, Japan
| | | | | | | | | |
Collapse
|
36
|
Miyazaki E, Sakaguchi M, Wakabayashi S, Shigekawa M, Mihara K. NHE6 protein possesses a signal peptide destined for endoplasmic reticulum membrane and localizes in secretory organelles of the cell. J Biol Chem 2001; 276:49221-7. [PMID: 11641397 DOI: 10.1074/jbc.m106267200] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The NHE6 protein is a unique Na(+)/H(+) exchanger isoform believed to localize in mitochondria. It possesses a hydrophilic N-terminal portion that is rich in positively charged residues and many hydrophobic segments. In the present study, signal sequences in the NHE6 molecule were examined for organelle localization and membrane topogenesis. When the full-length protein was expressed in COS7 cells, it localized in the endoplasmic reticulum and on the cell surface. Furthermore, the protein was fully N-glycosylated. When green fluorescent protein was fused after the second (H2) or third (H3) hydrophobic segment, the fusion proteins were targeted to the endoplasmic reticulum (ER) membrane. The localization pattern was the same as that of fusion proteins in which green fluorescent protein was fused after H2 of NHE1. In an in vitro system, H1 behaved as a signal peptide that directs the translocation of the following polypeptide chain and is then processed off. The next hydrophobic segment (H2) halted translocation and eventually became a transmembrane segment. The N-terminal hydrophobic segment (H1) of NHE1 also behaved as a signal peptide. Cell fractionation studies using antibodies against the 15 C-terminal residues indicated that NHE6 protein localized in the microsomal membranes of rat liver cells. All of the NHE6 molecules in liver tissue possess an endoglycosidase H-resistant sugar chain. These findings indicate that NHE6 protein is targeted to the ER membrane via the N-terminal signal peptide and is sorted to organelle membranes derived from the ER membrane.
Collapse
Affiliation(s)
- E Miyazaki
- Department of Molecular Biology, Graduate School of Medical Science, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | | | | | | | | |
Collapse
|
37
|
van der Vliet HN, Sammels MG, Leegwater AC, Levels JH, Reitsma PH, Boers W, Chamuleau RA. Apolipoprotein A-V: a novel apolipoprotein associated with an early phase of liver regeneration. J Biol Chem 2001; 276:44512-20. [PMID: 11577099 DOI: 10.1074/jbc.m106888200] [Citation(s) in RCA: 207] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Liver regeneration in response to various forms of liver injury is a complex process, which ultimately results in restoration of the original liver mass and function. Because the underlying mechanisms that initiate this response are still incompletely defined, this study was aimed to identify novel factors. Liver genes that were up-regulated 6 h after 70% hepatectomy (PHx) in the rat were selected by cDNA subtractive hybridization. Besides known genes associated with cell proliferation, several novel genes were isolated. The novel gene that was most up-regulated was further studied. Its mRNA showed a liver-specific expression and encoded a protein comprising 367 amino acids. The mouse and human cDNA analogues were also isolated and appeared to be highly homologous. The human gene analogue was located at an apolipoprotein gene cluster on chromosome 11q23. The protein encoded by this gene had appreciable homology with apolipoproteins A-I and A-IV. Maximal expression of the gene in the rat liver and its gene product in rat plasma was observed 6 h after PHx. The protein was present in plasma fractions containing high density lipoprotein particles. Therefore, we have identified a novel apolipoprotein, designated apolipoprotein A-V, that is associated with an early phase of liver regeneration.
Collapse
MESH Headings
- Amino Acid Sequence
- Amino Acids/chemistry
- Animals
- Apolipoprotein A-V
- Apolipoproteins
- Apolipoproteins A/biosynthesis
- Apolipoproteins A/blood
- Apolipoproteins A/chemistry
- Apolipoproteins A/genetics
- Apolipoproteins A/metabolism
- Base Sequence
- Blotting, Northern
- Blotting, Western
- Chromatography, Gel
- Chromosomes, Human, Pair 11
- DNA, Complementary/metabolism
- Humans
- Liver/physiology
- Male
- Mice
- Models, Genetic
- Molecular Sequence Data
- Nucleic Acid Hybridization
- RNA, Messenger/metabolism
- Rats
- Rats, Wistar
- Regeneration
- Sequence Homology, Amino Acid
- Time Factors
- Tissue Distribution
- Up-Regulation
Collapse
Affiliation(s)
- H N van der Vliet
- Department of Experimental Hepatology, Academic Medical Center, University of Amsterdam, Meibergdreef 9, Amsterdam 1105 AZ, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
38
|
Kida Y, Sakaguchi M, Fukuda M, Mikoshiba K, Mihara K. Amino acid residues before the hydrophobic region which are critical for membrane translocation of the N-terminal domain of synaptotagmin II. FEBS Lett 2001; 507:341-5. [PMID: 11696368 DOI: 10.1016/s0014-5793(01)03000-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We examined the fine structure of the type I signal-anchor sequence of synaptotagmin II, which has a 60-residue N-terminal domain followed by a hydrophobic region (H-region), focusing on the hinge region between the N-terminal and the H-regions. It was found that the charged or highly polar residues support the translocation of the N-terminal domain through the endoplasmic reticulum membrane at specific positions in the hinge. The residue requirement correlated with the turn propensity scale for transmembranes. It is suggested that a certain conformation, likely helical hairpin, in the hinge is critical for N-terminal domain translocation.
Collapse
Affiliation(s)
- Y Kida
- Department of Molecular Biology, Graduate School of Medical Science, Kyushu University, Fukuoka, Japan
| | | | | | | | | |
Collapse
|
39
|
Hetero-aggregation with sucrase affects the activity, stability and conformation of extra- and intra-cellular cellobiase in the filamentous fungus T. clypeatus. Enzyme Microb Technol 2001. [DOI: 10.1016/s0141-0229(01)00375-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
40
|
Conesa A, Punt PJ, van Luijk N, van den Hondel CA. The secretion pathway in filamentous fungi: a biotechnological view. Fungal Genet Biol 2001; 33:155-71. [PMID: 11495573 DOI: 10.1006/fgbi.2001.1276] [Citation(s) in RCA: 171] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The high capacity of the secretion machinery of filamentous fungi has been widely exploited for the production of homologous and heterologous proteins; however, our knowledge of the fungal secretion pathway is still at an early stage. Most of the knowledge comes from models developed in yeast and higher eukaryotes, which have served as reference for the studies on fungal species. In this review we compile the data accumulated in recent years on the molecular basis of fungal secretion, emphasizing the relevance of these data for the biotechnological use of the fungal cell and indicating how this information has been applied in attempts to create improved production strains. We also present recent emerging approaches that promise to provide answers to fundamental questions on the molecular genetics of the fungal secretory pathway.
Collapse
Affiliation(s)
- A Conesa
- Department of Applied Microbiology and Gene Technology, TNO Nutrition and Food Research, Zeist, 3700 AJ, The Netherlands
| | | | | | | |
Collapse
|
41
|
Gonzalez R, Andrews BA, Asenjo JA. Metabolic control analysis of monoclonal antibody synthesis. Biotechnol Prog 2001; 17:217-26. [PMID: 11312697 DOI: 10.1021/bp000165b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A general route for protein synthesis in eukaryotic cells has been proposed and applied to monoclonal antibody (MAb) synthesis. It takes into account transcription of the gene, binding of ribosomes to mRNA, and polypeptide elongation including binding to SRP (signal recognition particles) and SRP-receptor, competing translocation, folding and glycosylation, assembly of the heavy and light chains in a tetrameric protein and Golgi processing and secretion. A comprehensive model was built on the basis of the proposed pathway. The model takes into account the mechanism of each step. Metabolic control analysis (MCA) principles were applied to the general pathway using the proposed model, and control coefficients were calculated. The results show a shared flux control (of both pathway flux and flux ratio at the branch) among different steps, i.e., transcription, folding, glycosylation, translocation and building blocks synthesis. The steps sharing the control depend on the concentration of building blocks, pathway flux and levels of OST (oligosacharyl transferase), BiP (heavy chain binding protein) and PDI (protein disulfide isomerase). Model predictions compare well with experimental data for MAb synthesis, explaining the control structure of the route and the heterogeneity of the product and also addressing future targets for improvement of the production rate of MAbs.
Collapse
Affiliation(s)
- R Gonzalez
- Millenium Institute for Advanced Studies in Cell Biology and Biotechnology, Centre for Biochemical Engineering and Biotechnology, Department of Chemical Engineering, University of Chile, Beauchef 861, Santiago, Chile
| | | | | |
Collapse
|
42
|
Humphreys DP, Sehdev M, Chapman AP, Ganesh R, Smith BJ, King LM, Glover DJ, Reeks DG, Stephens PE. High-level periplasmic expression in Escherichia coli using a eukaryotic signal peptide: importance of codon usage at the 5' end of the coding sequence. Protein Expr Purif 2000; 20:252-64. [PMID: 11049749 DOI: 10.1006/prep.2000.1286] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We investigated the ability of signal peptides of eukaryotic origin (human, mouse, and yeast) to efficiently direct model proteins to the Escherichia coli periplasm. These were compared against a well-characterized prokaryotic signal peptide-OmpA. Surprisingly, eukaryotic signal peptides can work very efficiently in E. coli, but require optimization of codon usage by codon-based mutagenesis of the signal peptide coding region. Analysis of the 5' of periplasmic and cytoplasmic E. coli genes shows some codon usage differences.
Collapse
Affiliation(s)
- D P Humphreys
- Celltech-Chiroscience, 216 Bath Road, Slough, Berkshire, SL1 4EN, United Kingdom.
| | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Nakai K. Protein sorting signals and prediction of subcellular localization. ADVANCES IN PROTEIN CHEMISTRY 2000; 54:277-344. [PMID: 10829231 DOI: 10.1016/s0065-3233(00)54009-1] [Citation(s) in RCA: 201] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- K Nakai
- Human Genome Center, Institute of Medical Science, University of Tokyo, Japan
| |
Collapse
|
44
|
Lechner A, Schütze N, Siggelkow H, Seufert J, Jakob F. The immediate early gene product hCYR61 localizes to the secretory pathway in human osteoblasts. Bone 2000; 27:53-60. [PMID: 10865209 DOI: 10.1016/s8756-3282(00)00294-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The human cysteine-rich protein 61 (hCYR61) belongs to the growing CCN (CYR61/CTGF/NOV) family of immediate early genes, which modulate cell growth and differentiation. hCYR61 is regulated by 1alpha, 25-dihydroxyvitamin D(3) (1,25-(OH)(2)D(3)) and growth factors in fetal human osteoblasts (hFOB cells). The murine homologue CYR61 was characterized as an extracellular matrix-associated protein that modulates basic fibroblast growth factor signaling, angiogenesis, and binds to integrin alpha(v)beta(3). Here we report the intracellular localization of the human CYR61 gene product by overexpressing fusion proteins with green fluorescent protein (GFP) in primary osteoblasts and the hFOB cell line. Full-length hCYR61-GFP localizes to the Golgi apparatus and cytoplasmatic granules, indicating targeting to the secretory pathway. Secretion of hCYR61 from osteoblasts is verified by Western blot detection from cellular supernatants. A truncated hCYR61-GFP fusion protein containing only the 34 N-terminal amino acids of hCYR61 also localizes to the Golgi apparatus mainly in the perinuclear region, which suggests that the N-terminus of hCYR61 is sufficient to target the protein to the secretory pathway. In summary, our results present the first evidence that human CYR61 localizes to the secretory pathway in primary osteoblasts and hFOB cells, and that it is secreted from these cells. The N-terminal 34 amino acids of hCYR61 provide a sufficient Golgi targeting sequence. Together with the immediate early regulation of hCYR61 mRNA by 1,25-(OH)(2)D(3), this suggests that hCYR61 might function as an extracellular signaling molecule in human bone.
Collapse
Affiliation(s)
- A Lechner
- Department of Metabolism, Endocrinology and Molecular Medicine, Medizinische Poliklinik, Universität Würzburg, Germany
| | | | | | | | | |
Collapse
|
45
|
Bruneau N, Lombardo D, Levy E, Bendayan M. Roles of molecular chaperones in pancreatic secretion and their involvement in intestinal absorption. Microsc Res Tech 2000; 49:329-45. [PMID: 10820517 DOI: 10.1002/(sici)1097-0029(20000515)49:4<329::aid-jemt2>3.0.co;2-h] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This review focuses on the contribution of molecular chaperones in the secretory process of digestive enzymes and their interaction with enterocytes. By using biochemistry and immunocytochemistry, we have shown that Grp94, Cpn10, Cpn60, and protein disulfide isomerase (PDI) are present all along the rough endoplasmic reticulum-Golgi-granule secretory pathway of the pancreatic acinar cells and are secreted into the acinar lumen. Two other molecular chaperones, Grp78 and the Hsp70, appear to be restricted to the rough endoplasmic reticulum and the trans-Golgi apparatus, respectively. We have found that chaperones can be associated with pancreatic enzymes along the secretory pathway. Indeed, double immunogold and immunocoprecipitation revealed an association between Cpn60 and the colipase-dependent lipase (CDL) and between Grp94 and the bile salt-dependent lipase (BSDL). These complexes are secreted into the acinar lumen and diverted to the duodenal lumen. These findings led us to investigate these enzyme-chaperone complexes in intestinal tissue. Grp94, Cpn60, and PDI are present on microvilli and on the endosomal compartment of enterocytes. Furthermore, we have shown that the Grp94-BSDL complexes are internalized by enterocytes through classical endocytosis. Upon dissociation of the BSDL-Grp94 complex in the late endosome, BSDL is transferred to the basolateral membrane. We propose that Grp94 interacts with specific receptors and/or could force the associated protein to adopt a specific conformation that allows its binding to corresponding membrane receptors and its internalization by enterocytes. These two hypotheses need not to be exclusive. The existence of such a pancreatic secretion-intestinal absorption link speaks in favor of a coordinated functional connection between these two entities, through molecular chaperones, in order to optimize intestinal activities.
Collapse
Affiliation(s)
- N Bruneau
- Département de pathologie et biologie cellulaire, Faculté de médecine, Université de Montréal, Montréal, Québec, Canada H3C 3J7
| | | | | | | |
Collapse
|
46
|
Nash P, Barry M, Seet BT, Veugelers K, Hota S, Heger J, Hodgkinson C, Graham K, Jackson RJ, McFadden G. Post-translational modification of the myxoma-virus anti-inflammatory serpin SERP-1 by a virally encoded sialyltransferase. Biochem J 2000; 347:375-82. [PMID: 10749666 PMCID: PMC1220969 DOI: 10.1042/0264-6021:3470375] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
SERP-1 is a secreted serpin (serine-proteinase inhibitor) encoded by myxoma virus, a poxvirus pathogen of rabbits. SERP-1 is required for myxoma-virus virulence, and the purified protein has been shown to possess independent anti-inflammatory activity in animal models of restenosis and antigen-induced arthritis. As an inhibitor of serine proteinases, SERP-1 acts against tissue-type plasminogen activator, urokinase-type plasminogen activator, plasmin, thrombin and Factor Xa. In the present study, examination of SERP-1 glycosylation-site mutants showed that the N-linked glycosylation of Asn(172) was essential for SERP-1 secretion, whereas mutation of Asn(99) decreased secretion efficiency, indicating that N-linked glycosylation plays an essential role in the processing and trafficking of SERP-1. Furthermore, comparison of SERP-1 from wild-type myxoma virus and a virus containing a targeted disruption of the MST3N sialyltransferase locus demonstrated that SERP-1 is specifically modified by this myxoma-virus-encoded sialyltransferase, and is thus the first reported viral protein shown to by modified by a virally encoded glycosyltransferase. Sialylation of SERP-1 by the MST3N gene product creates a uniquely charged species of secreted SERP-1 that is distinct from SERP-1 produced from other eukaryotic expression systems, though this has no apparent effect upon the kinetics of in vitro proteinase inhibition. Rather, the role of viral sialylation of SERP-1 likely relates to masking antigenicity or targeting SERP-1 to specific sites of action in vivo.
Collapse
Affiliation(s)
- P Nash
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
| | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Ladunga I. Large-scale predictions of secretory proteins from mammalian genomic and EST sequences. Curr Opin Biotechnol 2000; 11:13-8. [PMID: 10679337 DOI: 10.1016/s0958-1669(99)00048-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Machine learning techniques have improved predictions of secretory proteins from protein, genomic and expressed sequence tag (EST) sequences. Artificial neural networks, physical sequence analysis using high-performance optimization, and hidden Markov models identify extremely variable signal peptides (the vehicles of protein transport across the endoplasmic reticulum membrane), transmembrane segments, and specific extracellular and intracellular domains as indicators of possible roles in the intercellular and intracellular chemical signaling pathways. The major role of peptide hormones, blood coagulation factors, carcinogenesis agents, and other secretory proteins in orchestrating multicellular life indicates pharmacological potential in the cure of major diseases and numerous biotechnological applications.
Collapse
Affiliation(s)
- I Ladunga
- Bioinformatics Department, SmithKline Beecham Pharmaceuticals, King of Prussia, PA 19406-0939, USA.
| |
Collapse
|
48
|
Abstract
Pulse and pulse-chase experiments have been performed to study L-[(35)S] methionine incorporation and protein secretion kinetics in Aspergillus oryzae. Pulse experiments confirmed the mechanism of methionine uptake reported previously for Penicillium chrysogenum (Benko et al., 1967). Pulse-chase experiments were carried out to investigate the alpha-amylase secretion kinetics in A. oryzae. No unglycosylated alpha-amylase was detected neither intracellularly nor extracellularly demonstrating that glycosylation was not the rate controlling step in the secretory pathway. The pulse chase experiments indicated that there are two pools of intracellular alpha-amylase: a fast secreted and a slow secreted. The secretion of those two pools were described with a kinetic model, which was fitted to the pulse chase experiments.
Collapse
Affiliation(s)
- A L Santerre Henriksen
- Center for Process Biotechnology, Department of Biotechnology, Building 223, Technical University of Denmark, DK-2800 Lyngby, Denmark.
| | | | | | | |
Collapse
|
49
|
Töhönen V, Osterlund C, Nordqvist K. Testatin: a cystatin-related gene expressed during early testis development. Proc Natl Acad Sci U S A 1998; 95:14208-13. [PMID: 9826679 PMCID: PMC24352 DOI: 10.1073/pnas.95.24.14208] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To isolate genes involved in morphogenic aspects of testis development, and which may act in cell signaling pathways downstream of the testis-determining gene Sry, we have developed a modified mRNA differential display method named signal peptide differential display. It was used to target those genes that encode proteins having a signal peptide sequence. By using this method, we isolated a gene named testatin. This gene was found to be related to a group of genes that encodes cysteine protease inhibitors known as cystatins. Cystatins and their target proteases have been associated with tumor formation and metastasis, but also are involved in natural tissue remodeling events such as bone resorption and embryo implantation. We show that testatin expression is restricted to fetal gonads and adult testis. Furthermore, testatin is expressed during testis cord formation in pre-Sertoli cells, believed to be the site of Sry action, at a time immediately after the peak of Sry expression. This finding suggests that testatin might be activated by transcription factors that are known to orchestrate the early testis development pathway. This gene therefore represents one of the putative downstream targets likely to have an essential role in tissue reorganization during early testis development.
Collapse
Affiliation(s)
- V Töhönen
- Department of Cell and Molecular Biology, Medical Nobel Institute, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | | | | |
Collapse
|