Extensive gene amplification and concerted evolution within the CPR family of cuticular proteins in mosquitoes

Annotation of the Anopheles gambiae genome has revealed a large increase in the number of genes encoding cuticular proteins with the Rebers and Riddiford Consensus (the CPR gene family) relative to Drosophila melanogaster. This increase reflects an expansion of the RR-2 group of CPR genes, particularly the amplification of sets of highly similar paralogs. Patterns of nucleotide variation indicate that extensive concerted evolution is occurring within these clusters. The pattern of concerted evolution is complex, however, as sequence similarity within clusters is uncorrelated with gene order and orientation, and no comparable clusters occur within similarly compact arrays of the RR-1 group in mosquitoes or in either group in D. melanogaster. The dearth of pseudogenes suggests that sequence clusters are maintained by selection for high gene-copy number, perhaps due to selection for high expression rates. This hypothesis is consistent with the apparently parallel evolution of compact gene architectures within sequence clusters relative to single-copy genes. We show that RR-2 proteins from sequence-cluster genes have complex repeats and extreme amino-acid compositions relative to single-copy CPR proteins in An. gambiae, and that the amino-acid composition of the N-terminal and C-terminal sequence flanking the chitin-binding consensus region evolves in a correlated fashion.     

Characterization of RR-1 and RR-2 cuticular proteins from Myzus persicae

A cDNA library for Myzus persicae has served to identify sequences coding for cuticular proteins (CPs) with RR-1 and RR-2 consensus. Two putative CPs showed a common RR-2 chitin binding domain (CBD) but differed in their C and N terminals. Two other predicted CPs showed a typical RR-1 CBD but differed in size and sequence of the C and N terminals. An additional sequence encoding for a protein that showed terminal amino acid repeats similar to those of putative CPs from M. persicae, but lacked the R & R consensus, was also described. A comparison of the sequences obtained from the cDNA library with those attained from the genomic DNA, confirmed their identity as cuticular proteins genes. Presence of introns was revealed in the Mpcp4 and Mpcp5 genes coding for CPs with an RR-1 consensus. The Mpcp4 has a single large intron, while the Mpcp5 has two shorter ones. Introns were not found in the Mpcp2 and Mpcp3 genes encoding for CPs with RR-2 consensus. Differences were also noticed for 3' UTR and 5' UTR of both the RR-1 and RR-2 CPs. CPs genes were expressed in bacteria, and the resulting protein was identified as a CP by amino acid sequencing.     

Gene within gene configuration and expression of the Drosophila melanogaster genes lethal(2)neighbour of tid [l(2)not] and lethal(2)relative of tid [l(2)rot]

In this paper, we describe the structure and temporal expression pattern of the Drosophila melanogaster genes l(2)not and l(2)rot located at locus 59F5 vis à vis the tumor suppressor gene l(2)tid described previously and exhibiting a gene within gene configuration. The l(2)not protein coding region, 1530 nt, is divided into two exons by an intron, 2645 nt, harboring the genes l(2)rot, co-transcribed from the same DNA strand, and l(2)tid, co-transcribed from the opposite DNA strand, located vis à vis. To determine proteins encoded by the genes described in this study polyclonal rabbit antibodies (Ab), anti-Not and anti-Rot, were generated. Immunostaining of developmental Western blots with the anti-Not Ab resulted in the identification of a 45-kDa protein, Not45, which is smaller than the Not56 protein predicted from the sequence. Its localization in endoplasmic reticulum (ER) was established by immunoelectron microscopy of Drosophila melanogaster Schneider 2 cells. Not45 shows significant homology to yeast ALG3 protein acting as a dolichol mannosyltransferase in the asparagine-linked glycosylation. It is synthesized ubiquitously throughout embryonic life. The protein predicted from the l(2)rot sequence, Rot57, shows a homology to the NS2B protein of the yellow fever virus1 (yefv1). The results of l(2)rot RNA analysis by developmental Northern blot and by in situ RNA localization, as well as the results of the protein analysis via Western blot and immunohistochemistry suggest that l(2)rot is transcribed but not translated. Since RNAs encoded by the genes l(2)tid and l(2)rot are complementary and l(2)rot is presumably not translated we performed preliminary experiments on the function of the l(2)rot RNA as a natural antisense RNA (asRNA) regulator of l(2)tid expression, expressed in the same temporal and spatial manner as the l(2)tid− and l(2)not RNA. l(2)tid knock-out by antisense RNA yielded late embryonic lethality resulting from multiple morphogenetic defects.     

普通烟草CESA基因家族成员的鉴定、亚细胞定位及表达分析

纤维素合成酶蛋白(cellulose-synthase proteins, CESA)是一类质膜定位蛋白,以蛋白复合体的形式存在于质膜上合成纤维素,在细胞壁建成和植物生长发育过程中起着非常重要的作用。本研究利用CESA蛋白保守域序列PF03552检索普通烟草(Nicotiana tabacum L.)蛋白序列,并通过拟南芥(Arabidopsis thaliana)10个CESA蛋白序列在普通烟草基因组数据库中利用TBLASTN程序进行比对,共获得21条NtCESA基因候选序列,对这些序列进行蛋白序列理化性质分析、系统进化树构建、基因结构分析、保守结构域及跨膜区分析和组织表达模式分析,并对NtCESA9和NtCESA14两个蛋白进行了亚细胞定位实验。结果表明：获得的21条NtCESA蛋白序列的理化性质相似;系统进化分析将21个NtCESA基因和10个AtCESA基因分成5个分支,每一个分支各成员之间的进化相对保守,基因结构类似,不同分支之间的基因结构差异也较小;NtCESA蛋白结构域相对保守,都含有CESA蛋白典型的N端锌指结构、C端跨膜区和DDD-QXXRW保守功能域;组织表达分析结果表明,大部分NtCESA基因在幼苗和成熟期烟草的根、叶、胚芽和愈伤组织中都有表达,同一个分支中的基因表达模式基本一致,并且NtCESA基因参与初/次生细胞壁纤维素的合成与该基因编码蛋白的跨膜区数目存在关联,表明NtCESA基因家族成员功能上的复杂性;亚细胞定位结果证实NtCESA9和NtCESA14为质膜定位蛋白。本研究为烟草CESA基因家族功能的深入研究奠定了基础。     

毛果杨nsLTP基因家族全基因组水平鉴定及其表达特性分析

植物非特异性脂质转移蛋白（non-specific lipid transfer proteins,nsLTP）是一类多基因家族编码碱性蛋白,负责脂肪酸体外结和与膜之间的磷脂转移,在植物生长发育和逆境胁迫响应中扮演着重要角色。目前为止,尚无模式植物毛果杨（Populus trichocarpa）nsLTP家族的研究报导。本研究从全基因组水平对PtrnsLTP家族成员的基因数量、亲缘关系、基因结构、编码蛋白保守基序等特性进行了分析,结果表明：PtrnsLTP家族共由39个基因组成,进化成5个亚家族,其中A亚族含有6个基因、B亚族含有2个、C亚族含有13个、D亚族含有3个、E亚族含有15个。PtrnsLTP家族包含7对旁系同源基因,其中1对大于1,6对Ka/Ks均远小于1,且这6对基因均处于同一个大的进化分支上,进化压力的不同导致基因间的功能出现了分化,编码蛋白均含有Motif 1和 Motif 2保守基序。利用qRT-PCR技术并结合杨树转录组数据对PtrnsLTP的组织表达与盐胁迫响应特性研究发现：各家族成员在毛果杨根、茎和叶中均有表达且经qRT-PCR技术验证后与网站预测结果基本吻合,有11、15和13个成员分别在根、茎和叶中有较高的表达,表明该基因家族参与了杨树不同组织的生长发育;NaCl胁迫下,该家族39个基因中分别有26个成员在根部、14个成员在叶部表达量随着胁迫时间的增加而升高,而32个基因在茎部表现为先升高后降低的趋势。本研究结果对于PtrnsLTP家族基因生物学功能的鉴定与盐胁迫响应基因资源的工作有着积极的推动作用。     

A functional role for Anopheles gambiae Arrestin1 in olfactory signal transduction

Insect sensory arrestins act to desensitize visual and olfactory signal transduction pathways, as evidenced by the phenotypic effects of mutations in the genes encoding both Arr1 and Arr2 in Drosophila melanogaster. To assess whether such arrestins play similar roles in other, more medically relevant dipterans, we examined the ability of Anopheles gambiae sensory arrestin homologs AgArr1 and AgArr2 to rescue phenotypes associated with an olfactory deficit observed in D. melanogaster arrestin mutants. Of these, only AgArr1 facilitated significant phenotypic rescue of the corresponding Drosophila arr mutant olfactory phenotype, consistent with the view that functional orthology is shared by these Arr1 homologs. These results represent the first step in the functional characterization of AgArr1, which is highly expressed in olfactory appendages of An. gambiae in which it is likely to play an essential role in olfactory signal transduction. In addition to providing insight into the common elements of the peripheral olfactory system of dipterans, this work validates the importance of AgArr1 as a potential target for novel anti-malaria strategies that focus on olfactory-based behaviors in An. gambiae.     

Mouse glandular kallikrein genes. Structure and partial sequence analysis of the kallikrein gene locus

Mouse glandular kallikreins are encoded by a family of closely linked genes which are located on chromosome 7 at a site corresponding to the genetically defined Tam-1, Prt-4, and Prt-5 loci. We have characterized 24 kallikrein genes by genomic cloning and restriction mapping of 310 kilobase pairs of BALB/c mouse DNA. Most of these genes are highly homologous, have the same exon/intron organization, and are linked in clusters of up to 11 genes. Partial sequence analysis of the kallikrein genes has facilitated identification of those members of the family for which protein sequence data exist and assignment of those which are pseudogenes or encode proteins of unknown function. We find that a maximum of 14 mouse kallikrein genes have the potential to encode functional proteins.     

青狗尾草RNAi途径相关基因的全基因组鉴定和表达分析

RNAi途径是RdDM途径的衍生途径,其中的AGO、DCL和RDR蛋白在植物的生长发育和响应非生物/生物胁迫过程中发挥重要作用。为了研究RNAi途径的3种主要蛋白在青狗尾草中的序列及结构特征,利用比较基因组学方法,在青狗尾草中鉴定到13个AGO基因、7个DCL基因和4个RDR基因,并对其蛋白质亚细胞定位、系统发育关系、保守结构域进行预测。同时,利用转录组数据分析RNAi途径的3类相关基因在青狗尾草的16种不同生长时期、不同生长条件下的表达模式。蛋白质结构域分析发现,SvDCL3b和SvRDR3缺少重要的结构域。转录组分析发现,SvAGO1b、SvDCL1a和SvRDR1在各家族中表达量较高,可能在RNAi途径中发挥主要作用,且大多数青狗尾草和谷子的同源基因间的表达模式基本一致。综上,本研究为理解RNAi途径的3种主要基因在调控青狗尾草的表观遗传修饰中的功能和作用提供初步的理论依据,为青狗尾草和谷子之间驯化的分子机制提供 参考。     

沙葱萤叶甲表皮蛋白基因的鉴定及表达谱分析

【目的】表皮蛋白是昆虫体壁的主要组成部分,在昆虫生长发育中起着重要的作用。本研究旨在鉴定沙葱萤叶甲Galeruca daurica表皮蛋白基因,分析其表达模式,以期为进一步研究其在沙葱萤叶甲生长发育中的作用提供必要的基础。【方法】根据本实验室组装的沙葱萤叶甲转录组测序数据,应用生物信息学方法鉴定表皮蛋白基因全长开放阅读框(ORF);采用RT-qPCR技术测定鉴定的8个表皮蛋白基因在沙葱萤叶甲不同发育阶段和3龄幼虫不同组织(头部、体壁、消化道和脂肪体)中的表达谱。【结果】基于转录组数据鉴定到8条沙葱萤叶甲表皮蛋白基因的开放阅读框(ORF)全长序列,命名为GdauCP1-8(GenBank登录号: MN629000-MN629007),ORF长417~810 bp,编码138~269个氨基酸,预测分子量为15~28 kD,等电点pI为4.45~8.62;具有16~20个氨基酸的信号肽;GdauCP1具有典型的跨膜结构,其余7个GdauCP蛋白无跨膜结构。同源序列比对和系统发育分析表明,GdauCP3与马铃薯甲虫Leptinotarsa decemlineata CP的氨基酸序列一致性最高,为60.00%;其余的GdauCPs与玉米根萤叶甲Diabrotica virgifera virgifera CP的氨基酸序列一致性最高,为58.52%~80.00%。GdauCP1-4属于RR-2亚家族,GdauCP5-7属于RR-1亚家族,GdauCP8的亚家族归属未确定。RT-qPCR分析表明,8个GdauCP基因在沙葱萤叶甲不同发育阶段及3龄幼虫不同组织内均有表达,且表达量存在显著差异。GdauCP2, GdauCP4, GdauCP5和GdauCP6在1龄幼虫期高表达,GdauCP3, GdauCP7和GdauCP8在蛹期高表达,GdauCP1在3龄第3天幼虫期高表达;除GdauCP2在成虫中表达水平较高外,其他GdauCP基因在成虫中的表达水平均很低。GdauCP1在头部和体壁中高表达,GdauCP2和GdauCP8在脂肪体中高表达,GdauCP3, GdauCP4, GdauCP6和GdauCP7在消化道中高表达,而GdauCP5在体壁中高表达。【结论】8个GdauCP基因在沙葱萤叶甲不同发育阶段和组织间差异表达,且表达模式不同,意味着不同GdauCP可能具有不同的功能。     

Distribution of cuticular protein mRNAs in silk moth integument and imaginal discs

The distributions of mRNAs for two cuticular proteins of Hyalophora cecropia were examined with RT-PCR and in situ hybridization. For major regions of larval and pupal cuticle, there was a strong correspondence between the type of cuticle and the predominant cuticular protein message found. Epidermal cells underlying soft cuticle had mRNA for HCCP12, with a RR-1 consensus attributed to soft cuticle, while the epidermal cells associated with hard cuticle had predominantly mRNA for HCCP66, a protein with the RR-2 consensus attributed to hard cuticle. Both messages were found in all areas of the pupal fore- and hind-wings, with modest area-specific difference in concentration being much less than differences in the relative abundance of these cuticular proteins.

mRNA for HCCP12 was present in imaginal discs of feeding larvae of H cecropia. Data from Bombyx mori available at SilkBase (http://www.ab.a.u-tokyo.ac.jp/silkbase/) revealed that imaginal discs from feeding larvae had abundant mRNA for RR-1 cuticular proteins, representing six distinct gene products. Only discs from spinning larvae had mRNAs that coded for RR-2 proteins arising from 10 distinct genes. Thus, lepidopteran wing imaginal discs can no longer be regarded as inactive in larval cuticle production.     

双叉犀金龟表皮蛋白TdCPR12611与TdCPR7854的表达纯化及特性分析

[目的]探析双叉犀金龟Trypoxylus dichotomus表皮蛋白的序列特征及生化性质.[方法]利用RT-PCR克隆双叉犀金龟表皮蛋白基因,利用生物信息学方法分析表皮蛋白的结构特征及系统发育;采用大肠杆菌Escherichia coli表达系统对双叉犀金龟表皮蛋白进行重组表达,并通过金属离子鳌合层析的方法对重组蛋...     

毛果杨CNGC家族全基因组鉴定及胁迫响应分析

植物环核苷酸门控离子通道（cyclic nucleotide-gated channels,CNGC）家族具有多种生物学功能,尤其是在植物的生长发育及逆境胁迫响应中发挥着重要的作用。本研究通过生物信息学方法及qRT-PCR对PtrCNGC家族成员蛋白的基本理化性质与结构特征、系统发育、基因结构和保守基序、启动子顺式作用元件,以及基因表达模式进行分析。结果表明：在毛果杨（Populus trichocarpa）全基因组中共鉴定出19个PtrCNGC基因,PtrCNGC家族成员可分为4个亚群（Ⅰ、Ⅱ、Ⅲ和Ⅳ亚群）,其中第Ⅳ亚群分为2个亚组（Ⅳa组和Ⅳb组）。PtrCNGC基因编码的蛋白均为碱性蛋白,此外,该家族仅有1个成员为疏水性蛋白,其余成员全部为亲水性蛋白。19个PtrCNGC不均匀地分布于毛果杨的11条染色体上,剩余8条染色体上没有成员分布。PtrCNGC家族包含7对同源基因且它们之间的K_a/K_s值均远小于1。PtrCNGC家族各亚群成员之间的基因结构、蛋白保守基序分布差异较小。启动子顺式作用元件预测分析发现,PtrCNGC基因序列启动子区域存在响应多种激素以及逆境胁迫相关的作用元件。qRT-PCR结果表明,PtrCNGC家族在不同组织中的表达具有特异性,在茎中的表达量较高,在根和叶中的表达量较低;在盐胁迫和干旱胁迫下,PtrCNGC家族同一分支上的多数成员表现出相似的表达模式。本研究结果为进一步研究毛果杨CNGC家族在非生物胁迫中的功能提供参考。     

Sequence and expression analysis of a Xenopus laevis cDNA which encodes a homologue of mammalian 14-3-3 zeta protein

We report the cloning and characterisation of a cDNA that encodes a novel member of the Xenopus laevis 14-3-3 protein family. Sequence analysis reveals that the cDNA-encoded protein shares 84% identity with the rat, human or sheep 14-3-3ζ isoform, and between 66% and 77% identity with bovine, human or rat β, bovine γ, human τ, Drosophila 14-3-3 and a previously isolated Xenopus member. The corresponding mRNA is present in all adult tissues examined with the highest levels in the brain. Although the gene is expressed throughout embryogenesis, higher levels of mRNA accumulate after gastrulation. Whole-mount in situ hybridisation on tailbud stage embryo reveals strong expression of the gene in the head, optic vesicles, spinal cord and branchial arches with weaker expression in the somites. In addition, expression along the notochord is observed at stage 45 (tadpole). This spatial and temporal expression profile along with recent studies implicating the importance of 14-3-3 proteins in the regulation of signal transduction pathways argues for a key role of this isoform in embryonic development.