A Subcellular Localization Survey for All SNARE Proteins in <i>Saccharomyces cerevisiae</i>

doi:10.13523/j.cb.20191006

China Biotechnology

2019, Vol. 39

Issue (10): 44-57 DOI: 10.13523/j.cb.20191006

A Subcellular Localization Survey for All SNARE Proteins in Saccharomyces cerevisiae

ZHANG Zheng-tan,ZHU Jing,XIE Zhi-ping(

)

State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology,Shanghai Jiao Tong University, Shanghai 200240, China

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Abstract

In eukaryotic cells, protein transport between membrane structures such as endoplasmic reticulum, Golgi, and plasma membrane is mainly achieved via vesicle budding and fusion. The SNARE protein family plays a key role in mediating the fusion of vesicles with the target membrane structure. In the model organism Saccharomyces cerevisiae, systematic studies of SNARE proteins in the whole genome are still lacking. A set of plasmids for the labeling of all 24 SNAREs in S. cerevisiae with GFP are constructed. Most of the plasmids employ endogenous promoters for expression, with only a few mildly overexpressed, thus avoiding potential mislocalization caused by high overexpression. The subcellular localization of each SNARE is verified by co-localization with organelle markers. Results indicate that the localization of three SNAREs differs from those in existing literature: Bos1 localizes to early Golgi; and Snc1 and Bet1 localize to the late Golgi/early endosomes. In addition, Sec9 is detected at the bud tip and septum. This is the first time that the localization of Sec9 in vegetative cells has been observed. It is also the first comprehensive experimental evaluation of yeast SNARE subcellular localization. Furthermore, the constructed plasmids constitute a convenient tool set for future yeast cell biology studies.

Key words： SNARE Subcellular localization Saccharomyces cerevisiae Colocalization

Received: 28 March 2019 Published: 12 November 2019

ZTFLH:

Q816

Corresponding Authors: Zhi-ping XIE E-mail: zxie@sjtu.edu.cn

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Cite this article:

ZHANG Zheng-tan,ZHU Jing,XIE Zhi-ping. A Subcellular Localization Survey for All SNARE Proteins in Saccharomyces cerevisiae. China Biotechnology, 2019, 39(10): 44-57.

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https://manu60.magtech.com.cn/biotech/10.13523/j.cb.20191006 OR https://manu60.magtech.com.cn/biotech/Y2019/V39/I10/44

Primer name			Primer sequence
Sec20 pro-F			TCCTGCAGCCCGGGGGATCCATTGTTTAATGTGGTCGTTGTAAC
Sec20 pro-R			AATTCTTCACCTTTAGACATAATCTTTAATGGCTTTATAGTTTGTT
Sec20-F			GGATCCCCGGGTTAATTAACATGGTCGTGACATTTTTGCAGGA
Sec20-R			ATACAGTTTTTTGCGGCCGCTCATAGCTCATCATGTGAGACG
Sec22 pro-F			TCCTGCAGCCCGGGGGATCCTCATAGATTTATCTTCATATGTTCT
Sec22 pro-R			AATTCTTCACCTTTAGACATCCCTACTTAATTGTGAGTGTG
Sec22-F			GGATCCCCGGGTTAATTAACATGATAAAGTCAACACTAATCTACA
Sec22-R			ATACAGTTTTTTGCGGCCGCCTATTTGAGGAAGATCCACCAG
Use1 pro-F			TCCTGCAGCCCGGGGGATCCAAGCCAAATCTGTTACGCACGG
Use1 pro-R			AATTCTTCACCTTTAGACATCTTGCCTTGCTATTATGTGTCC
Use1-F			GGATCCCCGGGTTAATTAACATGGCTGAAACTTCCAACGAC
Use1-R			ATACAGTTTTTTGCGGCCGCTTATAGGGCCGGGAATAATTGAA
Ufe1 pro-F			TCCTGCAGCCCGGGGGATCCAGCACCAAAATGCCTCCATTGA
Ufe1 pro-R			AATTCTTCACCTTTAGACATGAGTTAATAAGCTCTTCACTGC
Ufe1-F			GGATCCCCGGGTTAATTAACATGATGTCTGATTTAACACCAATAT
Ufe1-R			ATACAGTTTTTTGCGGCCGCTTAACCTACATAATCTAGGAACAAT
Sed5 pro-F			TCCTGCAGCCCGGGGGATCCCTATCGCCTCAAAGAACCACAT
Sed5 pro-R			AATTCTTCACCTTTAGACATGGGAGTTGTGTGGTATGGTGA
Sed5-F			GGATCCCCGGGTTAATTAACATGAACATAAAGGATAGAACTTCA
Sed5-R			ATACAGTTTTTTGCGGCCGCTTAATTGACTAAAACCCAAATAACG
Gos1 pro-F			TCCTGCAGCCCGGGGGATCCTGCCTGTTAGACACGAGATGTT
Gos1 pro-R			AATTCTTCACCTTTAGACATGTGGTGTGGTTGCTTGTCTGG
Gos1-F			GGATCCCCGGGTTAATTAACATGAGCTCACAACCGTCTTTCG
Primer name		Primer sequence
Gos1-R		ATACAGTTTTTTGCGGCCGCTTACCATGTGAAAAACAAAAACAGT
Bos1 pro-F		TCCTGCAGCCCGGGGGATCCACGTCTTCTATATCTGGGTTTTC
Bos1 pro-R		AATTCTTCACCTTTAGACATTCCCCCCTCAAATCAATATGATT
Bos1-F		GGATCCCCGGGTTAATTAACATGGTATGTTTGATCGCCGGA
Bos1-R		ATACAGTTTTTTGCGGCCGCCTATCTTAACCATTTCAACACATAA
Sft1 pro-F		TCCTGCAGCCCGGGGGATCCGGCGGAAAGTTAGGCCGACA
Sft1 pro-R		AATTCTTCACCTTTAGACATCGCTATGATGATTATATATTACCTT
Sft1-F		GGATCCCCGGGTTAATTAACATGTCAAATTCTAGGTATTCTCAG
Sft1-R		ATACAGTTTTTTGCGGCCGCCTAAAATAACTTAAACAGGGTATATA
Tlg1 pro-F		TCCTGCAGCCCGGGGGATCCGATAGTCCCCCATTTTTTTTTATGT
Tlg1 pro-R		AATTCTTCACCTTTAGACATTTGTTAAAGAAAGGATCTTAGCAAT
Tlg1-F		GGATCCCCGGGTTAATTAACATGAACAACAGTGAAGATCCGTT
Tlg1-R		ATACAGTTTTTTGCGGCCGCTCAAGCAATGAATGCCAAAACTAA
Tlg2 pro-F		TCCTGCAGCCCGGGGGATCCCACCCATTTAAATTTGACGATAAA
Tlg2 pro-R		AATTCTTCACCTTTAGACATGTTTGTAACGACTGCCTAGATC
Tlg2-F		GGATCCCCGGGTTAATTAACATGTTTAGAGATAGAACTAATTTATTT
Tlg2-R		ATACAGTTTTTTGCGGCCGCTCAAAGTAGGTCATCCAAAGCAT
Snc1 pro-F		TCCTGCAGCCCGGGGGATCCTAATATGTCCTTAGAATGGGGAA
Snc1 pro-R		AATTCTTCACCTTTAGACATGGACAATGAATACGTTGCGCTT
Snc1-F		GGATCCCCGGGTTAATTAACATGTCGTCATCTACTCCCTTTGA
Snc1-R		ATACAGTTTTTTGCGGCCGCCTATCGACTAAAGTGAACAGCAA
Snc2 pro-F		TCCTGCAGCCCGGGGGATCCGTGTTTCGTTAGGTGGGCCG
Snc2 pro-R		AATTCTTCACCTTTAGACATCGTTGCGCGTTCTTATTTTGTA
Snc2-F		GGATCCCCGGGTTAATTAACATGTCGTCATCAGTGCCATACG
Snc2-R		ATACAGTTTTTTGCGGCCGCTTAGCTGAAATGGACGACGATAG
Bet1 pro-F		TCCTGCAGCCCGGGGGATCCCCAGGCGACGTCAGAGATGA
Bet1 pro-R		AATTCTTCACCTTTAGACATCTGTGTAGCCTAGTGTTGTGA
Bet1-F		GGATCCCCGGGTTAATTAACATGAGTTCAAGGTATGAGAAATTAT
Bet1-R		ATACAGTTTTTTGCGGCCGCTTATGTAATCCATACCCAAAAAAATA
Vam3 pro-F		TCCTGCAGCCCGGGGGATCCGAAAACAAGGAAAAAACAACAGAA
Vam3 pro-R		AATTCTTCACCTTTAGACATAATCTCAACTTTCTGCAGTGGAT
Vam3-F		GGATCCCCGGGTTAATTAACATGTCCTTTTTCGACATCGAAG
Vam3-R		ATACAGTTTTTTGCGGCCGCCTAACTTAATACAGCAAGCAATAC
Vam7 pro-F		TCCTGCAGCCCGGGGGATCCGCCTATTCTTTCACCAAATTCAG
Vam7 pro-R		AATTCTTCACCTTTAGACATCAATATCAATTATCAACCCTTATATG
Vam7-F		GGATCCCCGGGTTAATTAACATGGCAGCTAATTCTGTAGGGA
Vam7-R		ATACAGTTTTTTGCGGCCGCTCAAGCACTGTTGTTAAAATGTCT
Nyv1 pro-F		TCCTGCAGCCCGGGGGATCCAAGGCGGCAAGACTTCAAGAAG
Nyv1 pro-R		AATTCTTCACCTTTAGACATTTGGTAAAAATATAAAAGTCCAAT
Nyv1-F		GGATCCCCGGGTTAATTAACATGAAACGCTTTAATGGTATGTATA
Nyv1-R		ATACAGTTTTTTGCGGCCGCTTACCACAGATAGAAAAACATGAAA
Primer name	Primer sequence
Vti1 pro-F	TCCTGCAGCCCGGGGGATCCATTGATTATCCTTCAAGTCCATC
Vti1 pro-R	AATTCTTCACCTTTAGACATAGTAAGCCATGCAGCAATGTAAA
Vti1-F	GGATCCCCGGGTTAATTAACATGAGTTCCCTATTAATATCATACG
Vti1-R	ATACAGTTTTTTGCGGCCGCTTATTTAAACTTTGAGAACAAAACTA
Pep12 pro-F	TCCTGCAGCCCGGGGGATCCTACTTAGTCCTTTGGTCAAAAATAT
Pep12 pro-R	AATTCTTCACCTTTAGACATCTCAACACAATTATTGTAGTAATTTA
Pep12-F	GGATCCCCGGGTTAATTAACATGTCGGAAGACGAATTTTTTGG
Pep12-R	ATACAGTTTTTTGCGGCCGCTTACAATTTCATAATGAGAAAAATAAAA
Syn8 pro-F	TCCTGCAGCCCGGGGGATCCTGAAAGCTCGTACTTCTGTCGC
Syn8 pro-R	AATTCTTCACCTTTAGACATACCGTGTGTGCTTACGCATCTA
Syn8-F	GGATCCCCGGGTTAATTAACATGGATGTGTTGAAGCTGGGTT
Syn8-R	ATACAGTTTTTTGCGGCCGCTTATAATACTAATAGAAGCAACAGG
Ykt6 pro-F	TCCTGCAGCCCGGGGGATCCTTCTTCTTCTCCATTATTATCTTCA
Ykt6 pro-R	AATTCTTCACCTTTAGACATTGCCAAAATAACTTCTCTAGTGAT
Ykt6-F	GGATCCCCGGGTTAATTAACATGAGAATCTACTACATCGGTG
Ykt6-R	ATACAGTTTTTTGCGGCCGCCTACATGATGATGCAACACGAAT
Sso1 pro-F	TCCTGCAGCCCGGGGGATCCTACCGAAGAAAGAATACGACGAT
Sso1 pro-R	AATTCTTCACCTTTAGACATTTGATTTGTTTCTATTTTTAATTGCC
Sso1-F	GGATCCCCGGGTTAATTAACATGAGTTATAATAATCCGTACCAG
Sso1-R	ATACAGTTTTTTGCGGCCGCTTAACGCGTTTTGACAACGGCT
Sso2 pro-F	TCCTGCAGCCCGGGGGATCCTATAAATATAATAATATTATTGATTAATTA
Sso2 pro-R	AATTCTTCACCTTTAGACATTGCTGCAATATTTGTGCGTGTAT
Sso2-F	GGATCCCCGGGTTAATTAACATGAGCAACGCTAATCCTTATGA
Sso2-R	ATACAGTTTTTTGCGGCCGCTTACTTTCTTGTTTCCACAACGG
Sec9 pro-F	TCCTGCAGCCCGGGGGATCCTCTCTCTCTCTCTCTACTTAACA
Sec9 pro-R	AATTCTTCACCTTTAGACATTCTTTTGGTGTCAATGGTGTATTA
Sec9-F	GGATCCCCGGGTTAATTAACATGGGATTAAAGAAATTTTTTAAGAT
Sec9-R	ATACAGTTTTTTGCGGCCGCCTATCTGATACCTGCCAACCTG
Spo20 pro-F	TCCTGCAGCCCGGGGGATCCAAAAAGCCGTTTGCGGAAAGCA
Spo20 pro-R	AATTCTTCACCTTTAGACATTATATATCTAAAAATGGCTATTCACA
Spo20-F	GGATCCCCGGGTTAATTAACATGGGGTTCAGAAAAATACTTGCTA
Spo20-R	ATACAGTTTTTTGCGGCCGCTCACCATCTTTTCCCGATCACT
BS-Ura-F	CCTTTTTTGCGAGGCATATTTATG
BS-Ura-R	GTAACTATTGAATTTTGTTTGGATTT
GFP-F	ATGTCTAAAGGTGAAGAATTATTCA
GFP-Fa6a-R	GTTAATTAACCCGGGGATCCGTCGACCTGCAGCGTACGAAGCTTTGTACAATTCATCCATACCATG
Stu1-F	CCAATTGAGGCCTTTTTTGCGAGGCATATTTAT
Stu1-R	AAAAAGGCCTCAATTGGCGCAGTAGCCTCA
Snab1-F	TAGTTACGTAGACGTCCTACGATTCCGCGG
Snab1-R	GGACGTCTACGTAACTATTGAATTTTGTTTGGATT

Table 1 DNA sequences of PCR primers

Table 2 Plasmids and restriction sites or PCR primers used to generate linear fragments for yeast transformation

Fig.1 A diagram of the GFP-SNARE series construction Fragments containing the SNARE gene promoter (SNAREpro), GFP ORF and SNARE protein ORF were amplified by the polymerase chain reaction (PCR). These fragments were inserted into the BS-Ura3Kl vector

Fig.2 SNAREs present on intracellular puncta Yeast cells were collected at mid-log phase and captured by fluorescence microscopy on Con A coated cover glass. Z-stacks containing 15 slices at 0.5μm step size were captured. Slice: A single representative slice; Z Projection: Maximal intensity projection of Z-stacks; DIC: Differential interference contrast

Fig.3 SNAREs present on larger organelles Images were captured and presented as in Fig. 1

Fig.4 SNAREs present on plasma membrane Images were captured and presented as in Fig. 1

Fig.5 SNAREs present on ER or in nucleus Images were captured and presented as in Fig.1, with the addition of a merge channel between green SNAREs and red organelle markers; mCherry-HDEL: ER marker; Nop56-DuDre:Nucleolus marker

Fig.6 SNAREs present on early Golgi Images were captured and presented as in Fig.5. Anp1-mCherry:Early Golgi marker; Sec7-DuDre:Late Golgi/early endosome marker; Snf7-mCherry:Late endosome marker

Fig.7 SNAREs present on late Golgi/early endosome Images were captured and presented as in Fig.5

Fig.8 SNAREs present on vacuole or late endosome Images were captured and presented as in Fig.5. Vph1-mCherry:Vacuole marker

Table 3 Subcellular localization of SNARE proteins in Saccharomyces cerevisiae


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