生物工程学报  2022, Vol. 38 Issue (1): 264-274
http://dx.doi.org/10.13345/j.cjb.210381
中国科学院微生物研究所、中国微生物学会主办
0

文章信息

王康, 杨民杰, 吴思宜, 刘庆丽, 曹士锋, 陈伟, 施丽愉
WANG Kang, YANG Minjie, WU Siyi, LIU Qingli, CAO Shifeng, CHEN Wei, SHI Liyu
桃漆酶基因家族鉴定及其与冷害褐变的关系
Identification of laccase gene family members in peach and its relationship with chilling induced browning
生物工程学报, 2022, 38(1): 264-274
Chinese Journal of Biotechnology, 2022, 38(1): 264-274
10.13345/j.cjb.210381

文章历史

Received: May 24, 2021
Accepted: July 9, 2021
Published: July 16, 2021
桃漆酶基因家族鉴定及其与冷害褐变的关系
王康 , 杨民杰 , 吴思宜 , 刘庆丽 , 曹士锋 , 陈伟 , 施丽愉     
浙江万里学院 生物与环境学院, 浙江 宁波 315100
摘要:为研究桃果实漆酶(PpLAC) 基因家族成员的功能,利用生物信息分析方法对桃果实LAC基因成员进行鉴定,分析不同品种桃果实低温贮藏和外源γ-氨基丁酸(γ-aminobutyric acid,GABA) 处理下的表达模式及其与冷害褐变的关系,为桃果实抗冷害褐变机制提供理论依据。研究从桃果实基因组筛选了26个漆酶基因,这些漆酶基因分布于6条染色体上,含有5–7个外显子,基因结构和保守基序较为相似。根据聚类分析结果将桃果实PpLAC基因家族成员分为7个亚族。通过良方水蜜桃、湖景水蜜桃以及外源GABA处理组的转录组测序结果分析,发现PpLAC7PpLAC9在低温贮藏下表达量呈上升模式,且与褐变指数呈现相同的趋势。GABA处理组减轻桃果实褐变程度,且PpLAC7PpLAC9的表达也被抑制,推测PpLAC7PpLAC9可能与桃果实冷害褐变有关。
关键词    漆酶家族    生物信息分析    冷害    褐变    
Identification of laccase gene family members in peach and its relationship with chilling induced browning
WANG Kang , YANG Minjie , WU Siyi , LIU Qingli , CAO Shifeng , CHEN Wei , SHI Liyu     
College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, Zhejiang, China
Abstract: The laccase (PpLAC) gene family members in peach fruit were identified and the relationship between their expression pattern and chilling induced browning were investigated. The study was performed using two varieties of peaches with different chilling tolerance, treated with or without exogenous γ-aminobutyric acid (GABA) during cold storage. Twenty-six genes were screened from the peach fruit genome. These genes were distributed on 6 chromosomes and each contained 5–7 exons. The PpLAC gene family members shared relatively similar gene structure and conserved motifs, and they were classified into 7 subgroups based on the cluster analysis. Transcriptome sequencing revealed that the expression levels of PpLAC7 and PpLAC9 exhibited an increasing pattern under low temperature storage, and displayed a similar trend with the browning index of peach fruit. Notably, GABA treatment reduced the degree of browning and inhibited the expression of PpLAC7 and PpLAC9. These results suggested that PpLAC7 and PpLAC9 might be involved in the browning of peach fruit during cold storage.
Keywords: peach    laccase family    bioinformatic analysis    chilling injury    browning    

漆酶是一种含有铜的氧化酶,属于铜蓝蛋白氧化酶家族[1],多数漆酶由铜离子活性中心、单一肽链以及糖基所构成,能氧化催化多种底物,包括酚类化合物、芳香胺、多环芳烃以及其他具有高氧化还原电位的化合物[2],已被应用在生物降解、食品工业、染料降解、生物燃料等诸多领域。漆酶首先从日本漆树的汁液中分离出来,研究发现这种具有许多独特催化特性的含铜蛋白质广泛分布于自然界生物中,如植物、真菌、细菌和昆虫等[3]

漆酶在植物生长过程中发挥着重要作用:拟南芥中AtLAC15参与种皮的着色和根系的伸长,AtLAC4AtLAC11AtLAC17与木质素聚合相关[4-5];水稻OsLAC13通过调节糖的转运和过氧化氢(H2O2) 的产生,对结实率起到重要作用[6];梨果实PbLAC1参与了木质素的生物合成和细胞壁的发育[7]。此外,漆酶在植物抗逆环境中也起到重要作用,在经非生物胁迫(如盐、干旱和重金属) 处理后,水稻OsLAC10可催化单木酚氧化产生木质素,而且OsLAC10的过表达增强了其对铜的耐受性,抑制了植物根中铜的积累[8]。水稻LACOsGhI1 (Os01g61160) 在拟南芥中异位表达时,可增强拟南芥对盐和干旱的耐受性[9];漆树RvLAC2[10]和玉米ZmLAC1[11]参与伤口修复和盐度反应。目前已在多个物种中克隆和鉴定出漆酶基因家族,其生物学功能已成为研究热点。

桃果实是一种典型的呼吸跃变型果实,在呼吸跃变前后会发生复杂的生理生化反应和代谢变化,品质迅速下降,不易贮藏[12]。低温是桃果实常见的贮藏方式。但低温贮藏下的桃果实易发生冷害,表现为果肉絮败、干化、粉质化、褐变等。其中褐变是较严重的一个问题,直接降低桃果实品质,影响消费者可接受程度。现有研究表明,漆酶可以催化表儿茶素之间的反应使苹果皮中呈现棕褐色,表明它可能是造成组织褐色的原因之一[13]。Fang等对采后荔枝褐变进行研究,发现荔枝漆酶在果皮褐变中起着降解花色素苷的作用[14]。在鸭梨果实中,漆酶与其果心褐变也有密切的关系[15]

γ-氨基丁酸(γ-aminobutyric acid, GABA) 作为非蛋白质氨基酸,它能够调节植物生长发育和响应胁迫反应的信号,在植物生理的信号转导中具有重要的调控功能[16]。因此许多研究已将GABA作为外源物质施用于植物,以抵抗生长发育过程中受到的逆境损害[17]。其中有研究表明,施用外源GABA可以提高西葫芦[18]、南果梨[19]、桃果实[20]、鲜切红掌花[21]的抗冷性,进而抑制其冷害褐变的产生。

本研究对桃果实漆酶基因家族成员进行鉴定和分析,并将其转录组结果和褐变指数关系进行分析,为后期在桃果实中展开对漆酶基因研究提供理论依据。

1 材料与方法 1.1 桃PpLAC基因家族成员信息获得及蛋白性质鉴定

利用桃基因库(http://www.plantgdb.org/PeGDB/) 以及本实验室桃果实发育时期转录组数据库筛选获得LAC基因家族候选基因,将获得的基因序列信息在NCBI进行BLAST比对(https://blast.ncbi.nlm.nih.gov/Blast.cgi),获得其基本信息,并对基因家族成员进行命名。利用在线软件Protparam (https://web.expasy.org/protparam) 分析漆酶基因家族成员的氨基酸数量、理论等电点和分子量大小等理化性质。利用在线软件SignalP-5.0 Server (http://www.cbs.dtu.dk/services/SignalP/) 进行信号肽预测。利用WoLF PSORT (https://wolfpsort.hgc.jp/) 进行亚细胞定位预测分析。通过NCBI搜集桃LAC基因在染色体上的位置及所在染色体的长度,使用MapInspect软件绘制染色体定位图。

1.2 桃基因结构、基因保守基序和进化树分析

利用GSDS2.0 (http://gsds.gao-lab.org/) 在线软件绘制基因结构图。利用MEME (https://meme-suite.org/meme/tools/meme) 在线网站进行蛋白保守基序预测,用Tbtools绘制蛋白保守基序图。利用MAGE7.0中的Clustal W对桃LAC成员以及拟南芥LAC成员进行序列比对,采用相邻连接法(neighbor-joining, NJ) 执行参数maximum composite likelihood,complete deletion和bootstrap 1 000次重复,构建系统进化树,用iTOL进行系统进化树图像绘制。

1.3 不同品种桃果实PpLAC家族基因在低温下与褐变的关系

以浙江省宁波市奉化县具有代表性的湖景和良方水蜜桃为试验材料,于硬熟期(盛花后105–120 d) 采收,选择大小均匀、成熟度一致、无病虫害、无机械伤的果实,当日尽快运回实验室。将湖景水蜜桃、良方水蜜桃用蒸馏水简单清洗,去除杂质,晾干后置于4 ℃下贮藏,在第14天和28天进行取样,取样后将部分桃果实转移至20 ℃,3 d后进行褐变指数的统计,4 ℃样品用液氮冷冻,作为不同品种实验样品,−80 ℃贮藏备用。再将剩余的湖景水蜜桃随机分为两组,对照组(CK):在蒸馏水中浸泡20 min;GABA处理组:在5 mmol/L GABA溶液中浸泡20 min。处理完的果实晾干后置于4 ℃下贮藏,在第14天和28天进行取样,取样后将部分桃果实转移至20 ℃,3 d后进行褐变指数的统计,4 ℃样品用液氮冷冻,作为GABA处理实验样品,−80 ℃贮藏备用。将贮藏的样品磨成粉末,用干冰保存,送至广州基迪奥生物科技有限公司进行转录组测序,用Tbtools将测序结果进行绘制。

桃果实褐变指数以直接评价果肉内部褐变程度进行测定,并记录计算[22]。随机取30个果实,分为3组,沿着果实缝合线纵切,褐变程度采用5级评分法,0=无(无褐变);1=褐变面积 < 15%;2=褐变面积介于15%–45%之间;3=褐变面积介于45%–70%之间;4=褐变面积 > 70%。计算公式如下:

褐变指数=∑((褐变级别×该级别果实个数)/ (4×测定果实个数))×100%。

2 结果与分析 2.1 PpLAC基因家族鉴定

表 1所示,以水蜜桃拉丁名Prunus persica简称为前缀,基因注释简称为后缀对基因家族成员进行命名。这26个LAC基因编码的氨基酸长度在558–586个氨基酸之间,分子量在61.24–64.99 kDa之间,等电点在5.11–9.85之间。对其信号肽进行预测,发现只有PpLAC11-1PpLAC15-3PpLAC15-5无信号肽,其他家族成员均存在信号肽(表 2),且稳定性较好,多数为亲水蛋白。对LAC基因进行染色体和亚细胞定位发现,LAC基因在染色体上呈不均匀分布,其多数分布在2、6和8号染色体上,少数分布在1、5和7号染色体上(图 1),PpLAC基因家族成员多数定位于叶绿体,部分定位于液泡、过氧化物酶体及细胞质等。

表 1 桃(Prunus persica) PpLAC漆酶基因家族成员基本信息 Table 1 PpLAC gene family members identified from the genome of peach (Prunus persica)
Gene ID Annotation Accession number Chr Molecular weight/KD Formula Names
ppa02720m laccase-4 XM_007220767.2 Chr2 61.24 C2794H4290N740O782S15 PpLAC4
ppa01742m laccase-17 XM_007207484.2 Chr6 64.28 C2956H4523N773O803S17 PpLAC17
ppa00364m laccase-4 XM_007204948.2 Chr6 60.77 C2762H4283N745O777S13 PpLAC4-1
ppa00357m laccase-11 XM_007204942.2 Chr6 62.27 C2840H4312N754O794S17 PpLAC11
ppa00329m laccase-2 XM_007207954.2 Chr6 64.56 C2962H4540N792O808S12 PpLAC2
ppa00330m laccase-17 XM_007208232.2 Chr6 64.99 C2970H4605N803O809S15 PpLAC17-1
ppa02244m laccase-4 XM_007207034.2 Chr6 61.63 C2794H4351N761O774S20 PpLAC4-2
ppa00359m laccase-11 XM_007198928.2 Chr8 62.16 C2842H4341N747O790S17 PpLAC11-1
ppa01554m laccase-11 XM_007200154.2 Chr8 62.20 C2846H4349N747O789S17 PpLAC11-2
ppa00371m laccase-17 XM_020566762.1 Chr6 64.49 C2964H4539N775O807S17 PpLAC17-2
ppa00357m laccase-11 XM_007204136.2 Chr7 65.07 C2968H4526N788O826S19 PpLAC11-3
ppa01686m laccase-14 XM_007227239.1 Chr1 64.12 C2938H4422N774O804S21 PpLAC14
ppa00334m laccase-12 XM_007218870.2 Chr2 64.07 C2883H4430N786O833S20 PpLAC12
ppa02133m laccase-6 XM_007220647.2 Chr2 63.60 C2890H4388N752O821S25 PpLAC6
ppa00352m laccase-15 XM_007220587.2 Chr2 62.94 C2875H4356N744O814S18 PpLAC15
ppa01988m laccase-1 XM_007210710.2 Chr5 65.50 C2984H4509N783O844S20 PpLAC1
ppa00354m laccase-15 XM_007204938.2 Chr6 63.05 C2881H4342N742O817S19 PpLAC15-1
ppa00331m laccase-17 XM_007207949.2 Chr6 64.45 C2952H4496N778O820S14 PpLAC17-3
ppa00358m laccase-7 XM_007204944.2 Chr6 61.87 C2805H4251N737O808S20 PpLAC7
ppa00358m laccase-9 XM_007199683.2 Chr8 62.27 C2817H4248N732O825S22 PpLAC9
ppa02508m laccase-15 XM_020570674.1 Chr8 61.26 C2816H4245N745O769S13 PpLAC15-2
ppa02532m laccase-15 XM_007199916.2 Chr8 62.34 C2810H4213N725O845S21 PpLAC15-3
ppa00366m laccase-9 XM_007199709.2 Chr8 61.26 C2757H4153N721O826S20 PpLAC9-1
ppa01480m laccase-15 XM_007200213.2 Chr8 62.54 C2819H4226N728O849S20 PpLAC15-4
ppa00358m laccase-9 XM_007199684.2 Chr8 62.06 C2805H4225N725O828S22 PpLAC9-2
ppa01612m laccase-15 XM_007200129.2 Chr8 64.10 C2920H4399N771O828S17 PpLAC15-5
表 2 桃(Prunus persica) PpLAC漆酶基因家族成员蛋白性质分析 Table 2 Characteristics of proteins encoded by PpLAC gene family members
Gene names Number of amino acids pI Instability index Aliphatic index Hydropathy index Signal peptide Subcellular localization
PpLAC4 558 9.02 27.92 86.49 –0.045 Yes Chloroplast
PpLAC17 581 9.30 29.06 87.57 –0.034 Yes Chloroplast
PpLAC4-1 559 9.31 30.38 88.75 –0.060 Yes Chloroplast
PpLAC11 564 8.41 30.08 81.26 –0.133 Yes Vacuole
PpLAC2 587 9.77 31.74 83.88 –0.092 Yes Chloroplast
PpLAC17-1 586 9.85 35.68 83.98 –0.156 Yes Chloroplast
PpLAC4-2 558 9.43 32.41 88.33 –0.083 Yes Chloroplast
PpLAC11-1 563 8.78 33.80 85.72 –0.079 No Chloroplast
PpLAC11-2 563 8.78 33.36 86.61 –0.074 Yes Chloroplast
PpLAC17-2 583 9.33 31.22 87.92 –0.027 Yes Chloroplast
PpLAC11-3 587 8.65 34.55 82.35 –0.107 Yes Cytoplasm
PpLAC14 568 8.98 38.73 76.02 –0.296 Yes Peroxisome
PpLAC12 583 8.53 35.19 80.81 –0.166 Yes Cytoplasm
PpLAC6 574 8.38 31.35 79.77 –0.134 Yes Chloroplast
PpLAC15 567 6.82 37.04 85.59 –0.118 Yes Vacuole
PpLAC1 582 7.06 36.01 75.86 –0.272 Yes Chloroplast
PpLAC15-1 567 6.64 35.85 82.01 –0.160 Yes Vacuole
PpLAC17-3 585 9.02 37.36 83.88 –0.072 Yes Vacuole
PpLAC7 563 5.95 36.48 87.26 –0.028 Yes Chloroplast
PpLAC9 564 5.93 30.44 79.34 –0.118 Yes Chloroplast
PpLAC15-2 542 8.71 31.24 79.65 –0.280 Yes Chloroplast
PpLAC15-3 569 5.11 34.58 76.47 –0.115 No Extracellular
PpLAC9-1 558 5.52 29.85 77.42 –0.140 Yes Extracellular
PpLAC15-4 569 5.29 34.53 75.59 –0.146 Yes Peroxisome
PpLAC9-2 564 5.58 31.98 79.54 –0.101 Yes Cytoplasm
PpLAC15-5 568 6.76 40.08 80.12 –0.271 No Peroxisome
图 1 PpLAC基因家族成员染色体定位 Fig. 1 Chromosomal location of the PpLAC family members.
2.2 PpLAC基因家族成员结构和保守基序分析

为进一步分析桃LAC的基因结构,将26条基因进行结构分析,PpLAC基因家族成员除了PpLAC14不含有非翻译区(untranslated region, UTR) 结构外(图 2),其余基因成员均含有内含子、外显子和UTR结构。其内含子数量4–6个,外显子数量5–7个,其中含5个内含子,6个外显子的成员最多。与其他植物中漆酶相类似,推断漆酶可能在不同的植物中具有保守的功能。

图 2 PpLAC家族基因结构分析图 Fig. 2 Analysis of the gene structure of PpLAC family gene members. : Exon/CDS; : non coding sequence/UTR; : intron/intron.

保守结构域分析发现PpLAC编码的蛋白属于铜氧还蛋白超家族。PpLAC15-2有2个结构域分别为Cu-oxidase_2和Cu-oxidase,而其余成员均含有3个保守结构域分别为Cu-oxidase_2、Cu-oxidase和Cu-oxidase_3,保守性较高。通过MEME网站以10个motif为条件进行预测,结果发现:PpLAC15-2含有5个motif (motif9、motif8、motif4、motif1、motif10) (图 3),其余25条基因家族成员均含有10个motif,说明该基因家族成员完整性好,较为保守。

图 3 PpLAC家族基因保守基序分析 Fig. 3 Analysis of the conserved motifs of PpLAC family gene members.
2.3 PpLAC基因家族成员系统进化树构建

将桃果实PpLAC基因家族成员与模式植物拟南芥漆酶(AtLAC) 基因家族进行系统进化树构建,根据聚类分析结果,将其分为7个亚族。如图 4所示:组1中含有1个桃漆酶基因和1个拟南芥基因(AtLAC6);组2含有10个桃漆酶基因和2个拟南芥基因(AtLAC14AtLAC15);组3含有1个桃漆酶基因和3个拟南芥基因(AtLAC7AtLAC8AtLAC9);组4含有1个桃漆酶基因和4个拟南芥基因(AtLAC3AtLAC13AtLAC5AtLAC12);组5中含有1个桃漆酶基因和1个拟南芥基因(AtLAC1);组6含有5个桃漆酶基因和2个拟南芥基因(AtLAC17AtLAC2);组7含有7个桃漆酶基因和4个拟南芥基因(AtLAC10AtLAC4AtLAC16AtLAC11)。在不同亚族中的拟南芥漆酶基因有着不同的功能,根据现有报道:组6和组7中的AtLAC17AtLAC4AtLAC11在拟南芥的木质素聚合中起到关键作用;组2的AtLAC15参与拟南芥种皮中类黄酮的氧化聚合[23];组3的AtLAC8AtLAC9是2种假定的高氧化还原电位植物漆酶;此外组4的AtLAC13AtLAC5AtLAC12对脱落酸(abscisic acid,ABA) 信号有响应。通过对比分析,进一步了解了PpLCA基因家族成员可能存在的功能和信息。

图 4 桃、拟南芥漆酶家族基因分子进化树分析 Fig. 4 Phylogenetic analysis of laccase family genes in peach and Arabidopsis. : peach laccase gene family members (PpLAC); : Arabidopsis laccase gene family members (AtLAC).
2.4 桃果实PpLAC家族基因在低温下与褐变的关系

不同品种桃果实良方水蜜桃、湖景水蜜桃在低温贮藏下褐变指数呈上升趋势,且外源GABA处理可以减轻桃果实的褐变程度,如图 5A5B所示。通过图 6A6B可以发现PpLAC7PpLAC9PpLAC9-1在低温下贮藏表达量显著高于其他家族成员的基因表达量,且PpLAC7PpLAC9基因表达量与良方水蜜桃、湖景水蜜桃褐变指数变化趋势一致,都随贮藏时间的增加而呈上升趋势。且外源GABA处理组PpLAC7PpLAC9基因表达量低于对照组,说明GABA处理能够减轻桃果实褐变及抑制PpLAC7PpLAC9基因的表达。由以上结果表明,PpLAC7PpLAC9基因可能调控桃果实冷害褐变的发生,且通过外源GABA的处理可以抑制其调控作用。

图 5 两品种桃果实(A) 及外源GABA处理(B) 的桃果实褐变指数 Fig. 5 Browning indexes of peach fruits from two cultivars (A) with/without exogenous GABA treatment (B). Different lowercase letters indicate significant differences at the 0.05 level (P < 0.05).
图 6 两品种桃果实及外源GABA处理桃果实(A) PpLAC家族成员基因表达(B) Fig. 6 Gene expression of PpLAC gene family members in peach fruits from two cultivars (A) with/without exogenous GABA treatment (B).
3 讨论

目前漆酶家族的基因组鉴定已相继在多个物种中被报道,包括柑橘[24]、拟南芥[4]、樱桃[25]、香蕉[26]、平菇[27]、水稻[8]等,但在桃果实中漆酶基因鉴定还未见报道。桃漆酶基因结构域特征与其他物种结构域特征基本一致,均属于铜蓝蛋白超家族,其基因结构、保守基序也与其他物种表现出相似的结果。通过分子进化树将桃漆酶家族基因分为7个不同的亚族,其中拟南芥基因家族成员在7个亚族中有不同的功能,包括木质素的聚合、种皮中类黄酮的氧化聚合以及对ABA信号的响应等,在亚族中与其亲缘关系较近的桃漆酶基因可能表现出相似的生物学功能。

桃果实是既属于呼吸跃变型果实也属于冷敏性果实,采后低温贮藏易出现冷害,表现为果肉褐变、絮败、粉质化和木质化等[28]。果肉褐变表现为果心周围组织产生棕褐色或者黑褐色,其形成的3大条件为酚类物质含量、多酚氧化酶活性和氧气供应。在有氧气的情况下,酚类物质被多酚氧化酶氧化生成醌类物质,醌类物质进一步通过聚合反应生成褐色聚合物[29-30]。漆酶作为多铜氧化酶属于多酚氧化酶的一种,具有很宽的底物范围[31],它不仅能够氧化邻二酚,而且还能氧化甲氧基取代的单酚、二胺和非芳香族化合物。本研究中,漆酶基因PpLAC7PpLAC9在湖景和良方低温贮藏下表达量随时间延长而上升,且两品种桃果实褐变指数在此期间也呈上升趋势,二者趋势一致。γ-氨基丁酸(GABA) 处理能提高谷氨酸脱羧酶、δ1-吡咯啉-5-羧酸合成酶和鸟氨酸δ-氨基转移酶的活性,降低脯氨酸脱氢酶的活性,显著增加内源性γ-氨基丁酸和脯氨酸的积累,从而减轻冷藏桃果实的冷害褐变[20]。本实验通过外源GABA处理减轻了桃果实的褐变程度,且漆酶基因PpLAC7PpLAC9的表达显著低于CK组。据此可以推断,可能在贮藏期间,桃果实在低温环境中组织受损,使酚类物质与漆酶接触,并在有氧气存在的情况下反应生成醌类物质,导致桃果实发生褐变,且外源GABA处理可以减轻褐变和抑制漆酶的活性。这与已有研究证明的漆酶可以使荔枝[14]、苹果[13]、龙眼[32]表皮以及葡萄汁[33]变为棕褐色的结果一致。因此可以推断漆酶作为多酚氧化酶很可能在桃果实低温贮藏产生褐变的过程中起到相同作用。此外,对PpLAC7PpLAC9基因上游启动子序列进行元件预测发现,发现其具有低温响应元件,说明PpLAC7PpLAC9基因会对低温胁迫产生响应。

4 结论

本研究对桃果实漆酶基因家族成员进行鉴定,分析其基本信息、理化性质、基因结构、染色体定位、亲缘关系以及在低温、GABA处理下与果实褐变的关系,为进一步研究桃果实中漆酶基因家族成员的功能提供理论基础。此外,从漆酶基因表达情况和果实褐变程度推测,PpLAC7PpLAC9可能参与了低温贮藏下桃果实产生冷害褐变的过程,并可能起到重要作用,但其具体作用机制仍需进一步探究。

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