家蚕触角蛋白质组学分析

家蚕触角蛋白质组学分析
家蚕触角蛋白质组学分析

Proteomic Analysis of Silkworm Antennae

Yunpo Zhao1&Haichao Li1&Xuexia Miao1

Received:3June2015/Revised:7September2015/Accepted:8October2015/Published online:29October2015 #Springer Science+Business Media New York2015

Abstract The silkworm Bombyx mori is an oligophagous in-sect that feeds mainly on mulberry leaves.The olfactory sys-tem of silkworm is a good model to study olfaction in Lepidoptera.Here,we carried out shotgun proteomic analysis and MS sequencing of the silkmoth antennae.A total of 364proteins were detected,77were female specific,143 were male specific,and144were expressed in both male and female antennae.Five odorant-binding proteins,two chemosensory proteins,and one olfactory receptor were identified.They may play a major role in the perception of odorants.An esterase and an aldehyde dehydrogenase were found only in male antennae.Glutathione S-transferases (GSTs)and cytochrome P450s,also found in silkworm anten-nae,may be involved in the degradation of xenobiotics. Additionally,antioxidation proteins and immunity proteins were identified.Juvenile hormone binding proteins(JHBP), juvenile hormone resistance protein II,and juvenile hormone episode hydrolase(JHEH)were found in the proteomic anal-ysis,which suggests that the antennae are a target for juvenile hormone in the silkworm.Our results provide insight into the expression of proteins in the antennae of silkworm and will facilitate the future functional analysis of silkworm antennae. Keywords Proteomics.Chemosensory.Odorant-binding proteins.Olfaction.Bombyx mori

Introduction

Insects use their antennae to sense odorant signals that guide their interactions with hosts and mating partners.They are able to locate hosts or edible plants by discriminating emitted volatiles.Odorants are sensed by olfactory receptor neurons (ORNs)housed in the sensilla on the antennae.ORNs express specific odorant receptors(ORs)and project axons to the brain (Leal2013).The silkworm,Bombyx mori is an oligophagous insect that feeds mainly on mulberry leaves(Horie1980). Silkworm is a well-established model for studying insect olfaction.

Female silkmoths produce two pheromones,bombykol and bombykal(Sakurai et al.2014).V olatile pheromones are hydro-phobic,thus,they need to bind to pheromone binding proteins (PBPs)to pass the aqueous sensillum lymph.Silkworm PBP was isolated from male antennae,but also found to be expressed in female antennae(Maida et al.1993).The PBP family is a subfamily of the odorant binding protein family in insects.The silkworm genome encodes forty-four candidate BmorOBP genes,with some expressed specifically in olfactory tissues,and others expressed more broadly in non-olfactory tissues(Gong et al.2009).

RNA-seq has been used widely to analyze the antennal transcriptome of various insects,including Drosophila melanoganster(Menuz et al.2014;Younus et al.2014), Anopheles gambiae(Rinker et al.2013),Spodoptera frugiperda(Legeai et al.2014),Helicoverpa armigera

Electronic supplementary material The online version of this article (doi:10.1007/s10886-015-0643-1)contains supplementary material, which is available to authorized users.

*Xuexia Miao

xxm@https://www.360docs.net/doc/6316580154.html,

Yunpo Zhao

ypzhao@https://www.360docs.net/doc/6316580154.html,

Haichao Li

lihaichao@https://www.360docs.net/doc/6316580154.html,

1Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology,Shanghai Institutes for Biological Sciences,Chinese Academy of Sciences,

Shanghai200032,People’s Republic of China

J Chem Ecol(2015)41:1037–1042 DOI10.1007/s10886-015-0643-1

(Liu et al.2012),Manduca sexta(Grosse-Wilde et al.2011). At the protein level,Anholt and Williams(2010)analyzed the soluble proteome of Drosophila antenna using a shotgun pro-teomic approach.The antennal proteomes of honeybees have been studied(Fang et al.2012;Feng et al.2011).Bombyx mori is an important model in chemosensory science,however,no antennal transcriptome or proteome of Bombyx mori is avail-able.Two draft genome sequence maps for Bombyx mori were published in2004(Mita et al.2004;Xia et al.2004),which propelled genomics and functional genomics research on Bombyx mori(Xia et al.2014).In this study,SDS-PAGE and shotgun LC-MS/MS were employed to characterize the proteome of the silkworm antennae.

Methods and Materials

Sample Preparation and Gel Electrophoresis Silkworm strain Dazao was obtained from the Sericulture Research Institute,Chinese Academy of Agriculture Sciences(SRI-CAAS),and reared on fresh mulberry leaves at26±1°C. The antennae of adult male and female silkmoths(1–3d-old) were cut and collected separately.The samples were snap-frozen in liquid nitrogen and then stored at?80°C.The an-tennae were ground to a powder in liquid nitrogen with a mortar and pestle.The resulting deep-frozen powder was transferred into400μl of lysis buffer(containing2.5% SDS,10%glycerin,5%β-mercaptoethanol,and50mM Tris-HCl pH8.8).The homogenate was kept for10min at room temperature,and then subjected to continued sonication treatment in an ice-bath four times,each time for15s with a 15s interval.The samples then were boiled for2min,and 60μg of protein were loaded into two lanes of an SDS-PAGE gel(8%stacking gel,12.5%resolving gel).The gels were stained with Coomassie Brilliant Blue R250(Sigma).

In-gel Digestion and Mass Spectrometry Each Coomassie-stained gel lane was manually cut into10slices(Fig.1).Each slice was cut into1×1mm pieces,and then subjected to in-gel tryptic digestion.The gel pieces were rinsed twice with Milli-Q water(Millipore)and destained thrice with25mM NH4HCO3in50%acetonitrile(ACN,Amersham).The sam-ples were evaporated to dryness in a vacuum centrifuge (Eppendorf)and then incubated with10mM dithiothreitol (BIO-RAD)in25mM NH4HCO3at56°C for1h with suf-ficient solution to cover the gel pieces.Upon cooling to room temperature,the same amount of55mM iodoacetamide in 25mM NH4HCO3was added,and the resulting solution was incubated at room temperature in the dark for45min. One hundred microliters of25mM NH4HCO3in50% ACN were added and incubated at room temperature with rotation for10min.This step was repeated twice to dehydrate the gel pieces.The samples were evaporated to dryness in the vacuum centrifuge.This was followed by the addition of tryp-sin(20ng/μl trypsin(sequence grade,Promega)in25mM NH4HCO3).The gel pieces were rehydrated at4°C for 30min.The extra trypsin solution was removed.The diges-tion was carried out at37°C overnight.The tryptic peptides mixture was extracted from the gel pieces with100μl Milli-Q water,followed by two extractions with5%trifluoroacetic acid(TFA,Fluka)in50%ACN solution.The pooled extracts were evaporated in a vacuum centrifuge to a volume of about 50μl.Liquid chromatography tandem mass spectrometry (LC–MS/MS)analysis was carried out as previously described.

Data Analysis A database was constructed with the protein sequences downloaded from the NCBInr database containing Bombyx and Drosophila,and the sequences from silkDB (https://www.360docs.net/doc/6316580154.html,/silkdb/doc/download.html).The 20raw datasets from the LC-MS/MS were searched against the database with the algorithm SEQUEST(Thermo Finnigan) on a local server.The mass tolerances of precursor and fragmentation ions were set to2and0.8,respectively.Only b and y ions were taken into account.The trypsin-cleavage was at both ends,and two missing cleavage sites were allowed. Static modification on cysteine(carbamidomethyl),and dynamic modification on methionine(oxidation)were set. Results

The Silkworm Antennal Proteome The proteomic profiles of the male and female silkworm antennae were obtained using a shotgun proteomics strategy and searched against an in-house compiled database.Tandem mass spectrometric analysis of eluted chromatographic peaks allowed for the identification of proteins through SEQUEST database search algorithms under stringent criteria.We identified265and

338 Fig.1SDS-PAGE analysis of the silkworm antenna proteome.The numbers indicate the ten slices used for sample fractionation prior to in-gel digestion

proteins from female and male silkworm antennae,respectively. Since the in-house database was built with protein sequences downloaded from the NCBI nr database and silkDB,there are identical protein sequences within this database.The redundant proteins were manually removed,and a total number of364 unique proteins were identified.Among them,77proteins are female specific,143are male specific,and144are expressed in both male and female antennae(Table1).Due to the limitations of the silkworm protein database,not all proteins had complete functional annotations.Some of those specific proteins identi-fied from the proteome of silkworm antennae are listed in Table2.

Odorant Binding Proteins,Chemosensory Proteins,and Olfactory Receptors Zhou et al.(2009)showed that the tran-scripts of BmorPBP1,BmorGOBP1,BmorGOBP2,and BmorABPx are highly enriched in the antennae of silkworm. In our proteomic analysis,we detected4of5OBPs (BmorPBP1,BmorGOBP2,BmorABPX,and antennal bind-ing protein precursor)both in male and female antennae (Table2).General odorant binding protein1(BmorGOBP1) was found only in female antennae.Chemosensory proteins (CSPs)are widely expressed in different tissues.The silk-worm genome encodes about20candidate CSPs(Gong et al.2007).In this study,two CSPs(CSP4and CSP13)were detected in the antennae(Table2).CSP4is transcribed pre-dominantly in the antennae,while CSP13is more widely expressed(Gong et al.2007).The olfactory receptor,OR45 (gi:162,461,258)was male-specific.

Esterases,Aldehyde Dehydrogenases,Glutathione S-Transferases(GSTs),Cytochrome P450s(CYPs),and Im-munity Related Proteins We identified an esterase and an aldehyde dehydrogenase in male antennae(Table2, Supplementary Table3).Glutathione S-transferases(GSTs) are a superfamily of multifunctional enzymes involved in the cellular detoxification of both xenobiotic and endobiotic com-pounds(Salinas and Wong1999).Twenty three GSTs have been identified in silkworm genome(Yu et al.2008).We detected8GSTs in silkworm antennae(Table2).Three GSTs(GST epsilon1,epsilon4,and omega1)were found specifically in female antennae,the remaining five(GST2, delta1,delta2,sigma1,and sigma2)were found in both male and female antennae.Antioxidant proteins(peroxiredoxin, thiol peroxiredoxin,thioredoxin peroxidase,thioredoxin-like protein,Mn superoxide dismutase,and glutathione peroxi-dase)also were detected in silkworm antennae(Table2). The cytochrome P450(CYP)superfamily is a large and di-verse group of enzymes that catalyze the oxidation of lipids, steroidal hormones,and xenobiotics(Guengerich2008).We identified7CYPs that showed a mutual exclusive pattern in male(4CYPs)and female(3CYPs)antennae(Table2).We also identified immune related proteins.Phenoloxidase is a key component of the insect immune system(Gonzalez-Santoyo and Cordoba-Aguilar2012).Phenoloxidase exists in circulating hemocytes and the cuticle in silkworm(Asano and Ashida2001;Ling et al.2005).GlcAT-S encodes a gly-cosyl transferase and its expression is induced by immune challenge(Kim et al.2005).

Juvenile Hormone-Related Proteins and Heat Shock-Related Proteins Juvenile hormone binding proteins(JHBPs), juvenile hormone resistance protein II,and juvenile hormone episode hydrolase(JHEH)were detected in the proteomic analysis,as were8heat shock-related proteins(Table2). Discussion

BmorPBP1,BmorPBP2,and BmorABPx bind the pheromone component bombykal equally well,whereas BmorGOBP2 binds bombykol more than it does to bombykal(Zhou et al. 2009).The silkworm genome encodes44odorant binding protein(OBP)genes(Gong et al.2009),however only a small number of OBPs were found in our proteomic analysis.These four OBPs are highly expressed(Zhou et al.2009).We spec-ulate the remaining OBPs are not expressed or at least are expressed at low levels in the antennae.The high concentra-tions of PBP1,ABPX,GOBP1,GOBP2,CSP4,and CSP13in silkworm antennae facilitate the perception of pheromones,as well as odorants(Supplementary Table1-3).The odorant binding protein OBP49a was able to attenuate nerve firings in sugar-activated taste sensory neurons when bitter com-pounds were combined with sucrose in Drosophila(Jeong et al.2013).It is surprising that an OBPs regulates taste per-ception.Silkworm feeds mainly on mulberry leaves.It will be interesting to determine whether these OBPs play a role in taste,as well as their primary role in olfaction.

The olfactory receptor,OR45was found only in male an-tennae.Wanner et al.(2007)showed that OR45is expressed in a female-biased manner,with7×higher levels of transcript found in female compare to male antennae by quantitative real-time PCR.There is a discrepancy between the proteomic data and this OR45transcript data.One possibility is that OR45transcript levels may not correlate well with its protein levels.In addition,we cannot rule out the possibility that female moth antennae also express the OR45protein but this was not detected in our study.Tanaka et al.(2009)also

Table1Numbers of proteins identified from female and male antennae

Female specific Male specific Common Total

SEQUEST84157181422 Redundancy removed77143144364

Table2The specific proteins identified from the proteome of Bombyx mori antennae

Accession number Annotation

Odorant binding proteins,chemosensory proteins,and olfactory receptors

gi|112,984,442*pheromone binding protein[Bombyx mori]

gi|112,984,426*general odorant-binding protein1precursor[Bombyx mori]

gi|112,984,436general odorant binding protein2[Bombyx mori]

BGIBMGA002626-PA antennal binding protein[Bombyx mori]

gi|164,448,664antennal binding protein precursor[Bombyx mori]

gi|112,983,094chemosensory protein4precursor[Bombyx mori]

gi|112,984,474chemosensory protein13precursor[Bombyx mori]

gi|162,461,258*olfactory receptor45[Bombyx mori]

Oxidative enzymes and defense mechanisms

gi|114,053,31126S protease regulatory subunit6B[Bombyx mori]

gi|112,983,471antichymotrypsin-1precursor[Bombyx mori]

gi|112,983,920chitinase-like protein EN03precursor[Bombyx mori]

BGIBMGA009106-PA glutathione S-transferase2[Bombyx mori]

gi|112,984,484glutathione S-transferase delta1[Bombyx mori]

gi|112,983,444glutathione S-transferase delta2[Bombyx mori]

gi|112,983,028glutathione S-transferase sigma1[Bombyx mori]

gi|160,333,678glutathione S-transferase sigma2[Bombyx mori]

gi|112,984,522glutathione S-transferase epsilon1[Bombyx mori]

gi|169,234,678glutathione S-transferase epsilon4[Bombyx mori]

gi|114,052,210glutathione S-transferase omega1[Bombyx mori]

BGIBMGA007286-PA ommochrome-binding protein[Bombyx mori]

gi|114,052,472peptidylprolyl isomerase B precursor[Bombyx mori]

gi|114,051,191peroxiredoxin[Bombyx mori]

gi|112,983,667phenoloxidase subunit1precursor[Bombyx mori]

gi|112,983,448phenoloxidase subunit2precursor[Bombyx mori]

gi|24,641,095stress-sensitive B,isoform B[Drosophila melanogaster]

gi|112,982,996thiol peroxiredoxin[Bombyx mori]

BGIBMGA013098-PA immune-related Hdd13[Hyphantria cunea]

gi|114,052,941thioredoxin peroxidase[Bombyx mori]

gi|148,298,796thioredoxin-like protein[Bombyx mori]

BGIBMGA003073-P A translationally controlled tumor protein[Bombyx mori]

gi|112,982,683catalase[Bombyx mori]

gi|19,921,004GlcAT-S,isoform B[Drosophila melanogaster]

gi|112,983,348glutathione peroxidase[Bombyx mori]

gi|190,341,026alpha-esterase25[Bombyx mori]

gi114052408mitochondrial aldehyde dehydrogenase[Bombyx mori]

gi|160,358,387cytochrome P450CYP6AE9[Bombyx mori]

gi|168,823,415cytochrome P450CYP366A1precursor[Bombyx mori]

gi|119,226,184cytochrome P4506AB4[Bombyx mori]

gi|162,462,656cytochrome P450,family307,subfamily a,polypeptide1precursor[Bombyx mori]

BGIBMGA002272-PA cytochrome P450[Bombyx mori]

gi|160,333,255CYP6AE family cytochrome P450CYP6AE21[Bombyx mori]

gi|163,838,680cytochrome P450CYP4G25[Bombyx mori]

BGIBMGA011085-PA putative toll[Danaus plexippus]

BGIBMGA006920-P A PREDICTED:similar to leucine-rich repeats and immunoglobulin-like domains3[Tribolium castaneum] Juvenile hormone related proteins

BGIBMGA004613-PA takeout/JHBP like protein[Papilio xuthus]

gi|112,983,194juvenile hormone binding protein an-0921precursor[Bombyx mori]

analyzed OR45transcription in male and female moth anten-nae.Although they did not quantify this,they did not see female biased transcription of OR45(Tanaka et al.2009).

Pheromones are thought to diffuse through100?-wide pore tubules in the cuticular wall of sensilla to enter the recep-tor lymph(Steinbrecht1980;V ogt and Riddiford1981).Thus, the receptor lymph is also exposed to oxidative stress and xenobiotic challenge.Rapid clearing of xenobiotics,as well as residual pheromone,from the sensilla is very important to the animal.Esterases are involved in pheromone degradation in insects.An esterase from female antennae of another moth was found to bind and degrade pheromone(Supplementary Table2;V ogt and Riddiford1981),and a male-specific ester-ase can also degrade pheromone(Supplementary Table3; Ishida and Leal2005;V ogt and Riddiford1981).Since the silkworm sex pheromone comprises an alcohol(bombykol) and an aldehyde(bombykal),sex pheromone components are unlikely to be a substrate for alpha-esterase25.An alde-hyde dehydrogenase was identified,however,in male anten-nae.Rybczynski et al.(1990)reported that a130kDa alde-hyde oxidase enriched in male antennae was able to metabo-lize bombykal.GSTs catalyze xenobiotic and endobiotic com-pound detoxification by conjugation with reduced glutathi-one,GSH(Salinas and Wong1999).They also are involved in regulating cell signaling pathways(Cho et al.2001).An antennal-specific GST can modify trans-2-hexenal,a plant derived green leaf aldehyde(Rogers et al.1999).Eight GSTs were identified in our proteomic analysis,three of them were female specific.Tan et al.(2014)described BmGSTD4, which was highly expressed and specific to male silkmoth antenna.However,BmGSTD4was not identified in our re-search.This suggests a limitation of the proteomics approach. Nevertheless,both studies revealed that some GSTs are highly expressed in silkmoth antennae.Anti-microbial peptide (AMP)genes are constitutively expressed in Spodoptera frugiperda antennae and palps at high levels(Legeai et al. 2014).Immunity-related proteins also were found in our study.This suggests that immunity pathways are activated in insect antennae.What is the importance of activating immu-nity pathways in the olfactory organs?Do they play a role in the odorants perception?It will be interesting to determine whether AMPs also are activated in silkmoth antennae and which transcription factor(s)regulate their expression.GSTs, oxidative enzymes,CYPs,and immunity proteins likely work together to maintain a favorable environment in the antennal hemolymph,which enables the insects to detect pheromones and plant volatiles in a very sensitive way.

JHBPs may protect JHs from nonspecific degradation and nonspecific adsorption,and transport JHs to the appropriate cellular compartment,while Juvenile hormone resistance pro-tein II and JHEH regulate JH titer(Suzuki et al.2011;Touhara and Prestwich1993).Expression of such proteins in silkworm antenna suggest that antennae are a target organ for JH,and that JH may play a role in the silkworm olfactory system.In honeybee,JH has a profound effect on short term olfactory memory(Maleszka and Helliwell2001).JH also induces GST activity(Wu and Lu2008).

Acknowledgments This work is funded by the National Basic Re-search Program of China(2015CB755703),grants from NSFC (31172152and31402012)and CAS(KSZD-EW-Z-021-2-1).

Author contributions X.M.designed the experiment and wrote the manuscript.Y.Z.and H.L.performed experiments and analyzed the data. Compliance with Ethical Standards

Conflict Interests The authors declare no conflict interests.

Table2(continued)

Accession number Annotation

gi|169,234,671juvenile hormone resistance protein II[Bombyx mori]

gi|112,984,538juvenile hormone epoxide hydrolase precursor[Bombyx mori]

gi|112,983,082cytosolic juvenile hormone binding protein36kDa subunit[Bombyx mori]

Heat shock proteins

BGIBMGA007950-P A heat shock protein70–3[Bombyx mori]

gi|28,571,719heat shock protein cognate4,isoform E[Drosophila melanogaster]

BGIBMGA004540-P A heat shock protein hsp19.9[Bombyx mori]

gi|112,983,414heat shock protein hsp21.4[Bombyx mori]

gi|112,982,828heat shock cognate protein[Bombyx mori]

gi|112,983,55690-kDa heat shock protein[Bombyx mori]

gi|112,983,152heat shock protein20.4[Bombyx mori]

gi|148,298,772heat shock protein70B[Bombyx mori]

*Bold font entries designate proteins found in both female and male antennal extracts;*underlined entries indicate proteins found in female antennae only;*italic font indicates proteins found in male antennal extracts only

References

Anholt RRH,Williams TI(2010)The soluble proteome of the drosophila antenna.Chem Senses35:21–30

Asano T,Ashida M(2001)Cuticular pro-phenoloxidase of the silkworm, bombyx Mori-purification and demonstration of its transport from hemolymph.J Biol Chem276:11100–11112

Cho SG,Lee YH,Park HS,Ryoo K,Kang KW,Park J,Eom SJ, Kim MJ,Chang TS,Choi SY,Shim J,Kim K,Dong M,Lee MJ, Kim SG,Ichijo H,Choi EJ(2001)Glutathione S-transferase Mu modulates the stress-activated signals by suppressing apoptosis signal-regulating kinase1.J Biol Chem276:12749–12755

Fang Y,Song FF,Zhang L,Aleku DW,Han B,Feng M,Li JK(2012) Differential antennal proteome comparison of adult honeybee drone, worker and queen(apis mellifera L.).J Proteome75:756–773 Feng M,Song FF,Aleku DW,Han B,Fang Y,Li JK(2011)Antennal proteome comparison of sexually mature drone and forager honey-bees.J Proteome Res10:3246–3260

Gong DP,Zhang HJ,Zhao P,Lin Y,Xia QY,Xiang ZH(2007) Identification and expression pattern of the chemosensory protein gene family in the silkworm,bombyx Mori.Insect Biochem Mol Biol37:266–277

Gong DP,Zhang HJ,Zhao P,Xia QY,Xiang ZH(2009)The odorant binding protein gene family from the genome of silkworm,bombyx Mori.BMC Genomics10:332.doi:10.1186/1471-2164-10-332 Gonzalez-Santoyo I,Cordoba-Aguilar A(2012)Phenoloxidase:a key component of the insect immune system.Entomol Exp Appl142: 1–16

Grosse-Wilde E,Kuebler LS,Bucks S,V ogel H,Wicher D,Hansson BS (2011)Antennal transcriptome of manduca sexta.Proc Natl Acad Sci U S A108:7449–7454

Guengerich FP(2008)Cytochrome P450and chemical toxicology.Chem Res Toxicol21:70–83

Horie Y(1980)Recent advances in sericulture.Annu Rev Entomol25: 49–71

Ishida Y,Leal WS(2005)Rapid inactivation of a moth pheromone.Proc Natl Acad Sci U S A102:14075–14079

Jeong YT,Shim J,Oh SR,Yoon HI,Kim CH,Moon SJ,Montell C (2013)An odorant-binding protein required for suppression of sweet taste by bitter chemicals.Neuron79:725–737

Kim T,Yoon J,Cho HS,Lee WB,Kim J,Song YH,Kim SN,Yoon JH, Kim-Ha J,Kim YJ(2005)Downregulation of lipopolysaccharide response in drosophila by negative crosstalk between the AP1and NF-kappa B signaling modules.Nat Immunol6:211–218

Leal WS(2013)Odorant reception in insects:roles of receptors, binding proteins,and degrading enzymes.Annu Rev Entomol 58:373–391

Legeai F,Gimenez S,Duvic B,Escoubas JM,Grenet ASG,Blanc F, Cousserans F,Seninet I,Bretaudeau A,Mutuel D et al(2014) Establishment and analysis of a reference transcriptome for spodoptera frugiperda.BMC Genomics15:704.doi:10.1186/1471-2164-15-704

Ling E,Shirai K,Kanehatsu R,Kiguchi K(2005)Reexamination of phenoloxidase in larval circulating hemocytes of the silkworm, bombyx Mori.Tissue Cell37:101–107

Liu Y,Gu SH,Zhang YJ,Guo YY,Wang GR(2012)Candidate olfaction genes identified within the helicoverpa armigera antennal tran-scriptome.PLoS One7:e48260

Maida R,Steinbrecht A,Ziegelberger G,Pelosi P(1993)The pheromone bindingpProtein of bombyx-mori-purification,characterization and immunocytochemical localization.Insect Biochem Mol Biol23: 243–253

Maleszka R,Helliwell P(2001)Effect of juvenile hormone on short-term olfactory memory in young honeybees(apis mellifera).Horm Behav 40:403–408Menuz K,Larter NK,Park J,Carlson JR(2014)An RNA-seq screen of the drosophila antenna identifies a transporter necessary for ammo-nia detection.PLoS Genet10:e1004810

Mita K,Kasahara M,Sasaki S,Nagayasu Y,Y amada T,Kanamori H,Namiki N,Kitagawa M,Y amashita H,Y asukochi Y and others.2004.The genome sequence of silkworm,bombyx Mori.DNA Res11:27–35. Rinker DC,Zhou XF,Pitts RJ,Rokas A,Zwiebel LJ,Consortium A (2013)Antennal transcriptome profiles of anopheline mosquitoes reveal human host olfactory specialization in anopheles gambiae.

BMC Genomics14:749.doi:10.1186/1471-2164-14-749

Rogers ME,Jani MK,V ogt RG(1999)An olfactory-specific glutathione-S-transferase in the sphinx moth manduca sexta.J Exp Biol202: 1625–1637

Rybczynski R,V ogt RG,Lerner MR(1990)Antennal-specific phero-mone-degrading aldehyde oxidases from the moths antheraea-polyphemus and bombyx-mori.J Biol Chem265:19712–19715 Sakurai T,Namiki S,Kanzaki R(2014)Molecular and neural mecha-nisms of sex pheromone reception and processing in the silkmoth bombyx Mori.Front Physiol5:125

Salinas AE,Wong MG(1999)Glutathione S-transferases-a review.Curr Med Chem6:279–309

Steinbrecht RA(1980)Cryofixation without cryoprotectants.Freeze sub-stitution and freeze-etching of an insect olfactory receptor.Tissue Cell12:73–100

Suzuki R,Fujimoto Z,Shiotsuki T,Tsuchiya W,Momma M,Tase A, Miyazawa M,Y amazaki T(2011)Structural mechanism of JH delivery in hemolymph by JHBP of silkworm,bombyx Mori.Sci Rep1:133 Tan X,Hu XM,Zhong XW,Chen QM,Xia QY,Zhao P(2014)Antenna-specific glutathione S-transferase in male silkmoth bombyx Mori.Int J Mol Sci15:7429–7443

Tanaka K,Uda Y,Ono Y,Nakagawa T,Suwa M,Yamaoka R,Touhara K (2009)Highly selective tuning of a silkworm olfactory receptor to a key mulberry leaf volatile.Curr Biol19:881–890

Touhara K,Prestwich GD(1993)Juvenile-hormone epoxide hydrolase.

Photoaffinity-labeling,purification,and characterization from to-bacco hornworm eggs.J Biol Chem268:19604–19609

V ogt RG,Riddiford LM(1981)Pheromone binding and inactivation by moth antennae.Nature293:161–163

Wanner KW,Anderson AR,Trowell SC,Theilmann DA,Robertson HM, Newcomb RD(2007)Female-biased expression of odourant recep-tor genes in the adult antennae of the silkworm,bombyx Mori.Insect Mol Biol16:107–119

Wu MC,Lu KH(2008)Juvenile hormone induction of glutathione S-transferase activity in the larval fat body of the common cutworm, spodoptera litura(Lepidoptera:noctuidae).Arch Insect Biochem Physiol68:232–240

Xia QY,Zhou ZY,Lu C,Cheng DJ,Dai FY,Li B,Zhao P,Zha XF,Cheng TC,Chai CL,…Yang H(2004)A draft sequence for the genome of the domesticated silkworm(bombyx Mori).Science306:1937–1940 Xia QY,Li S,Feng QL(2014)Advances in silkworm studies accelerated by the genome sequencing of bombyx Mori.Annu Rev Entomol59: 513–536

Younus F,Chertemps T,Pearce SL,Pandey G,Bozzolan F,Coppin CW, Russell RJ,Maibeche-Coisne M,Oakeshott JG(2014)Identification of candidate odorant degrading gene/enzyme systems in the anten-nal transcriptome of Drosophila melanogaster.Insect Biochem Mol Biol53:30–43

Yu QY,Lu C,Li B,Fang SM,Zuo WD,Dai FY,Zhang Z,Xiang ZH (2008)Identification,genomic organization and expression pattern of glutathione S-transferase in the silkworm,bombyx Mori.Insect Biochem Mol Biol38:1158–1164

Zhou JJ,Robertson G,He XL,Dufour S,Hooper AM,Pickett JA,Keep NH,Field LM(2009)Characterisation of bombyx Mori odorant-binding proteins reveals that a general odorant-binding protein dis-criminates between sex pheromone components.J Mol Biol389: 529–545

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名词解释 蛋白质组学:是研究与基因对应的蛋白质组的学科。指一种基因组所表达的全套蛋白质,即包括一个基因组、一种细胞或组织,乃至一种生物所表达的全部蛋白质。 双向电泳原理:双向一般是指第一向为等点聚焦(IEF),根据蛋白质等电点进行分离;第二向为SDS凝胶电泳(SDS-PAGE),根据蛋白质的相对分子量进行分离。 三步纯化策略:第一步粗提,浓缩,稳定蛋白,去除蛋白酶,使用梯度洗脱来增加捕获步骤的速度和容量;第二步中度纯化,去除主要杂质,一般需要连续梯度洗脱; 第三步精纯,最终去除痕量杂质,如目标蛋白的结构变体。 高效液相色谱:是一种以高压输出液体为流动相的色谱技术。在技术上采用高压输液泵、高效固定相和高灵敏度检测器,克服了经典液相色谱固定相柱效低,分析周期 长的缺点,具有分析速度快、分离效率高、检出极限地的特点。 吸附色谱:吸附色谱系色谱法之一种,利用固定相吸附中对物质分子吸附能力的差异实现对混合物的分离,吸附色谱的色谱过程是流动相分子与物质分子竞争固定相吸 附中心的过程。 PCR扩增:即聚合酶链式反应,是体外酶促合成特异DNA片段的一种方法,由高温变性、低温退火(复性)及适温延伸等反应组成一个周期,循环进行,使目的DNA 得以迅速扩增,具有特异性强、灵敏度高、操作简便、省时等特点。 基因组文库:基因文库是指整套由基因组DNA片段插入克隆载体获得的分子克隆的总和。 广义的基因文库指来于单个基因组的全部DNA克隆,理想情况下应含有这一 基因组的全部DNA序列(遗传信息),这种基因文库常通过鸟枪法获得。 狭义的基因文库有基因组文库和cDNA文库之分。 cDNA文库:按构建基因文库的类似方法对cDNA进行克隆,获得的克隆总称。 基因芯片:基因芯片又叫DNA芯片(DNA chip),DNA微阵列(DNA microarray), DNA集微芯片(DNA microchip),寡核苷酸阵列(oligonucleotide array)是一种将核酸分子杂交原理与微电子技术相结合而形成的高新生物技术。将靶标样品核酸或探针中的任一方按阵列形式固定在固相载体(硅片、尼龙膜、聚丙烯膜、硝酸纤维素膜、玻璃片等)上,另一方用荧光分子标记后,加样至微阵列上杂交,然后用荧光扫描或摄像技术记录,通过计算机软件分析处理,获得样品中大量的基因序列和表达信息。 基因敲除(gene knock out):又称基因打靶(gene targeting),是指用外源的DNA与受体细

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蛋白质组学与分析技术课复习思考 一、名词解释 1、蛋白质组学: 蛋白质组学是研究与基因对应的蛋白质组的学科,蛋白质组(proteome)一词,源于蛋白质(protein)与基因组(genome)两个词的杂合,意指“一种基因组所表达的全套蛋白质”,即包括一种细胞乃至一种生物所表达的全部蛋白质。 2、二维(双向)电泳原理: 根据蛋白质的等电点和相对分子质量的特异性将蛋白质混合物在第一个方向上按照等电点高低进行分离,在第二个方向上按照相对分子质量大小进行分离。二维电泳分离后的蛋白质点经显色,通过图象扫描存档,最后是呈现出来的是二维方向排列的,呈漫天星状的小原点,每个点代表一个蛋白质。 3、三步纯化策略: 第一步:粗提。纯化粗样快速浓缩(减少体积) 和稳定样品(去除蛋白酶) 最适用层析技术: 离子交换/疏水层析 第二步:中度纯化。去除大部分杂质 最适用层析技术: 离子交换/疏水层析 第三步:精细纯化。达到最终纯度(去除聚合物,结构变异物) 最适用层析技术:凝焦过滤/离子交换/疏水层析/反相层析 4、高效纯化策略 在三步纯化蛋白质过程中,同时考虑到纯化的速度、载量、回收率及分辨率的纯化策略。5、离子交换色谱: 离子交换色谱中的固定相是一些带电荷的基团,这些带电基团通过静电相互作用与带相反电荷的离子结合。如果流动相中存在其他带相反电荷的离子,按照质量作用定律,这些离子将与结合在固定相上的反离子进行交换。固定相基团带正电荷的时候,其可交换离子为阴离子,这种离子交换剂为阴离子交换剂;固定相的带电基团带负电荷,可用来与流动相交换的离子就是阳离子,这种离子交换剂叫做阳离子交换剂。阴离子交换柱的功能团主要是-NH2,及-NH3 :阳离子交换剂的功能团主要是-SO3H及-COOH。其中-NH3 离子交换柱及-SO3H离子交换剂属于强离子交换剂,它们在很广泛的pH范围内都有离子交换能力;-NH2及-COOH 离子交换柱属于弱离子交换剂,只有在一定的pH值范围内,才能有离子交换能力。离子交换色谱主要用于可电离化合物的分离,例如,氨基酸自动分析仪中的色谱柱,多肽的分离、蛋白质的分离,核苷酸、核苷和各种碱基的分离等。 6、吸附色谱 吸附色谱系色谱法之一种,利用固定相吸附中对物质分子吸附能力的差异实现对混合物的分离,吸附色谱的色谱过程是流动相分子与物质分子竞争固定相吸附中心的过程。洗脱次序∶一般为正相,即:极性低的先被洗脱。 7、PCR扩增 PCR技术(polymerase chain reaction)技术能把单个目的基因大量扩增,这个方法必须在已知基因序列或已知该基因所翻译的氨基酸序列。进而推断出因序列的情况下使用。PCR 的每次扩增循环包括三步:1)变性,在高温下把双链靶DNA拆开;2)在较低的温度下使

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第35卷 第1期2011年1月 南京林业大学学报(自然科学版) Journa l o fN anji n g Forestry Un i v ersity (Natural Sc ience Ed ition) V o.l 35,N o .1Jan .,2011 htt p ://www.n l dxb .com [do :i 10.3969/.j issn .1000-2006.2011.01.024] 收稿日期:2009-12-31 修回日期:2010-10-26 基金项目:国家自然科学基金项目(31000287);江苏省高校自然科学基础研究项目(10KJ B220002) 作者简介:甄艳(1976)),副教授,博士。*施季森(通信作者),教授。E-m ai:l js h @i n jfu .edu .cn 。 引文格式:甄艳,施季森.质谱技术在蛋白质组学研究中的应用[J].南京林业大学学报:自然科学版,2011,35(1):103-108. 质谱技术在蛋白质组学研究中的应用 甄 艳,施季森 * (南京林业大学,林木遗传与生物技术省部共建教育部重点实验室,江苏 南京 210037) 摘要:随着蛋白质组学研究的迅速发展,质谱技术已成为应用于蛋白质组学研究中的强有力工具和核心技术。质谱技术的先进性在于为蛋白质组学研究提供的通量和分子信息。笔者重点概述了基于质谱路线的蛋白质组学研究,介绍了基于质谱的定量蛋白质组学﹑翻译后修饰蛋白质组学、定向蛋白质组学、功能蛋白质组学以及基于串联质谱技术的蛋白质组学数据解析的研究 进展。 关键词:质谱;蛋白质组学;定量蛋白质组学;翻译后修饰;定向蛋白质组学;功能蛋白质组学中图分类号:Q81 文献标志码:A 文章编号:1000-2006(2011)01-0103-06 Application of m ass spectro m etry i n proteo m ics studies Z HEN Yan ,SH I Jisen * (K ey Labo ra t o ry o f F orest G eneti cs and B i o techno l ogy M i n istry o f Educati on , N an ji ng Forestry U n i versity ,N an ji ng 210037,Chi na) Abstrac t :W ith the rap i d develop m ent o f pro teo m i cs ,m ass spec trom etry i s m aturi ng to be a po w erfu l too l and core tech -nology fo r proteo m ics st udies dur i ng the recen t years .The super i or ity o fm ass spectrom etry lies i n providi ng the through -pu t and the m olecu lar infor m ati on ,w hich no other techno logy can be m a tched i n proteom ics .In th i s rev ie w,w e m ade a g lance on the outli ne o fm ass spectrome try -based proteo m ics .A nd then w e addressed on t he advances o f data ana l y si s o f m ass spec trom etry -based proteom ics ,quantitati ve m ass spectro m etry -based pro teom i cs ,post -translati onal m odificati ons based m ass spectrom etry ,targeted proteo m ics and functiona l proteo m ics based -mass spectrome try .K ey word s :m ass spectrome try;proteo m ics ; quantitative pro teom i cs ; post -trans l ation m odifica ti on ; targ eted pro - teo m i cs ;f uncti ona l proteom ics 蛋白质组学(Pr o teo m ics)是从整体水平上研究细胞内蛋白质的组成、活动规律及蛋白质与蛋白质的相互作用,是功能基因组学时代一门新的学科。 目前蛋白质组学的研究主要有两条路线:一是基于双向电泳的蛋白质组学;二是基于质谱的蛋白质组学,其中基于双向电泳的蛋白质组学研究路线最终也离不开质谱技术的应用。自20世纪80年代末,两种质谱软电离方式即电喷雾电离(electro spray ion izati o n,ESI )和基质辅助激光解析离子化(m a -tri x assisted laser desorpti o n i o nization ,MALD I)的发明和发展解决了极性大、热不稳定蛋白质和多肽分 析的离子化和分子质量大的测定问题[1] ,蛋白质组学研究中常用的质谱分析仪包括离子阱(ion trap ,I T),飞行时间(ti m e of fli g h,t TOF),串联飞行时间(TOF -TOF),四级杆/飞行时间(quadr upo le /TOF hybrids),离子阱/轨道阱(I T /orbitrap hybri d )和离子阱/傅里叶变换串联质谱分析仪(I T /Four i e r transfor m ioncyclotron resonance m ass spectro m eters hybr i d s ,I T /FT M S),这些质谱仪具有不同的灵敏度、分辨率、质量精确度和产生不同质量的M S /M S 谱[2] 。质谱作为蛋白质组学研究的一项强有力的工具日趋成熟,并作为样品制备及数据分析的信息学工具被广泛地应用。因此,有学者指出质谱技术 已在蛋白质组学研究中处于核心地位[3] 。目前在通量及所包含的分子信息内容上,基于质谱的蛋白质组学技术在细胞生物学研究中可以鉴定和量化

质谱技术在蛋白质组学研究中的应用_甄艳

第35卷 第1期2011年1月 南京林业大学学报(自然科学版) J o u r n a l o f N a n j i n g F o r e s t r y U n i v e r s i t y (N a t u r a l S c i e n c e E d i t i o n ) V o l .35,N o .1 J a n .,2011 h t t p ://w w w .n l d x b .c o m [d o i :10.3969/j .i s s n .1000-2006.2011.01.024]  收稿日期:2009-12-31 修回日期:2010-10-26  基金项目:国家自然科学基金项目(31000287);江苏省高校自然科学基础研究项目(10K J B 220002) 作者简介:甄艳(1976—),副教授,博士。*施季森(通信作者),教授。E -m a i l :j s h i @n j f u .e d u .c n 。  引文格式:甄艳,施季森.质谱技术在蛋白质组学研究中的应用[J ].南京林业大学学报:自然科学版,2011,35(1):103-108. 质谱技术在蛋白质组学研究中的应用 甄 艳,施季森 * (南京林业大学,林木遗传与生物技术省部共建教育部重点实验室,江苏 南京 210037) 摘要:随着蛋白质组学研究的迅速发展,质谱技术已成为应用于蛋白质组学研究中的强有力工具和核心技术。质谱技术的先进性在于为蛋白质组学研究提供的通量和分子信息。笔者重点概述了基于质谱路线的蛋白质组学研究,介绍了基于质谱的定量蛋白质组学﹑翻译后修饰蛋白质组学、定向蛋白质组学、功能蛋白质组学以及基于串联质谱技术的蛋白质组学数据解析的研究 进展。 关键词:质谱;蛋白质组学;定量蛋白质组学;翻译后修饰;定向蛋白质组学;功能蛋白质组学中图分类号:Q 81 文献标志码:A 文章编号:1000-2006(2011)01-0103-06 A p p l i c a t i o n o f m a s s s p e c t r o m e t r y i n p r o t e o m i c s s t u d i e s Z H E NY a n ,S H I J i s e n * (K e y L a b o r a t o r y o f F o r e s t G e n e t i c s a n d B i o t e c h n o l o g y M i n i s t r y o f E d u c a t i o n , N a n j i n g F o r e s t r y U n i v e r s i t y ,N a n j i n g 210037,C h i n a ) A b s t r a c t :W i t ht h e r a p i d d e v e l o p m e n t o f p r o t e o m i c s ,m a s s s p e c t r o m e t r y i s m a t u r i n g t o b e a p o w e r f u l t o o l a n dc o r e t e c h -n o l o g y f o r p r o t e o m i c s s t u d i e s d u r i n g t h e r e c e n t y e a r s .T h e s u p e r i o r i t y o f m a s s s p e c t r o m e t r y l i e s i n p r o v i d i n g t h e t h r o u g h -p u t a n d t h e m o l e c u l a r i n f o r m a t i o n ,w h i c hn o o t h e r t e c h n o l o g y c a n b e m a t c h e di np r o t e o m i c s .I nt h i s r e v i e w ,w e m a d e a g l a n c e o n t h e o u t l i n e o f m a s s s p e c t r o m e t r y -b a s e d p r o t e o m i c s .A n dt h e nw e a d d r e s s e d o n t h e a d v a n c e s o f d a t a a n a l y s i s o f m a s s s p e c t r o m e t r y -b a s e dp r o t e o m i c s ,q u a n t i t a t i v em a s ss p e c t r o m e t r y -b a s e dp r o t e o m i c s ,p o s t -t r a n s l a t i o n a l m o d i f i c a t i o n s b a s e d m a s s s p e c t r o m e t r y ,t a r g e t e d p r o t e o m i c s a n df u n c t i o n a l p r o t e o m i c s b a s e d -m a s s s p e c t r o m e t r y . K e yw o r d s :m a s ss p e c t r o m e t r y ;p r o t e o m i c s ;q u a n t i t a t i v ep r o t e o m i c s ;p o s t -t r a n s l a t i o n m o d i f i c a t i o n ;t a r g e t e d p r o -t e o m i c s ;f u n c t i o n a l p r o t e o m i c s 蛋白质组学(P r o t e o m i c s )是从整体水平上研究细胞内蛋白质的组成、活动规律及蛋白质与蛋白质的相互作用,是功能基因组学时代一门新的学科。目前蛋白质组学的研究主要有两条路线:一是基于双向电泳的蛋白质组学;二是基于质谱的蛋白质组学,其中基于双向电泳的蛋白质组学研究路线最终也离不开质谱技术的应用。自20世纪80年代末,两种质谱软电离方式即电喷雾电离(e l e c t r o s p r a y i o n i z a t i o n ,E S I )和基质辅助激光解析离子化(m a -t r i x a s s i s t e d l a s e r d e s o r p t i o n i o n i z a t i o n ,M A L D I )的发明和发展解决了极性大、热不稳定蛋白质和多肽分 析的离子化和分子质量大的测定问题[1] ,蛋白质组学研究中常用的质谱分析仪包括离子阱(i o n t r a p ,I T ),飞行时间(t i m e o f f l i g h t ,T O F ),串联飞行时间(T O F -T O F ),四级杆/飞行时间(q u a d r u p o l e /T O F h y b r i d s ),离子阱/轨道阱(I T /o r b i t r a ph y b r i d ) 和离子阱/傅里叶变换串联质谱分析仪(I T /F o u r i e r t r a n s f o r m i o n c y c l o t r o nr e s o n a n c em a s s s p e c t r o m e t e r s h y b r i d s ,I T /F T M S ),这些质谱仪具有不同的灵敏度、分辨率、质量精确度和产生不同质量的M S /M S 谱[2] 。质谱作为蛋白质组学研究的一项强有力的工具日趋成熟,并作为样品制备及数据分析的信息学工具被广泛地应用。因此,有学者指出质谱技术 已在蛋白质组学研究中处于核心地位[3] 。目前在通量及所包含的分子信息内容上,基于质谱的蛋白质组学技术在细胞生物学研究中可以鉴定和量化

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蛋白质组学及其主要技术

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