4种模式植物LRR Ⅷ-2亚家族基因的鉴定和进化历史分析

全基因组重复与串联重复是发生基因重复的重要机制,也是基因组和遗传系统多样化的重要动力。LRR-RLK编码富含亮氨酸重复的类受体蛋白激酶,是被子植物进化史上发生大规模扩张而形成的多基因家族。拟南芥(Arabidopsis thaliana)AtLRR-RLK包含15个亚家族,AtLRRⅧ-2是其中发生串联重复比例最高的亚家族。通过分析拟南芥、杨树(Populustrichocarpa)、葡萄(Vitis vinifera)和番木瓜(Carica papaya) 4种模式植物中LRR Ⅷ-2亚家族基因的扩张及差异保留情况,结果显示, LRR Ⅷ-2在杨树中的扩张程度最高,在拟南芥和葡萄中的扩张程度居中,但在番木瓜中发生丢失。拟南芥、杨树和葡萄LRR Ⅷ-2亚家族具有旁系同源基因对,但在番木瓜中未发现旁系同源基因。除杨树中的1对旁系同源基因外, 4种模式植物中LRR Ⅷ-2亚家族的旁系和直系同源基因都受到较强的纯化选择作用。对LRR Ⅷ-2亚家族进化历史的深入分析有助于理解基因重复在植物进化中的作用和意义,可为预测同源基因功能及解析其它基因家族进化历史提供参考。     

植物富含亮氨酸重复序列型类受体蛋白激酶的生物学功能

介绍了植物富含亮氨酸重复序列(leucine-rich repeat,LRR)型类受体蛋白激酶概念、最近发现的这类蛋白激酶的亚结构域特征;总结了目前已确定其功能的LRR型类受体蛋白激酶,并分别阐述了它们在参与植物抗逆性反应、发育调控及激素的信号转导等过程中的生物学功能;着重介绍和讨论了LRR型类受体蛋白激酶复合物之间及其与下游成分KAPP之间互作而产生信号传递的分子机理.最后展望了LRR型类受体蛋白激酶生物学功能、信号转导机制、以及应用于生产实践的研究前景.     

植物抗病基因的进化

植物抗病基因在进化中形成了几种共有的进化形式。植物祖先抗病基因的复制创造了新基因座。基因间和基因内重组导致了变异,也导致了新特异性抗病基因的产生。另外,与特异性识别相关的富含亮氨酸重复区顺应于适应性选择。同样,类转座元件在抗病基因座中的插入加速了抗病基因的进化。随着抗病基因的进化,抗病反应也呈现出多样化,代表着植物与病原物动态进化的不同阶段。     

高等植物的LRR蛋白:结构与功能

ＬＲＲ结构存在于细胞定位和功能上各不相同的多种蛋白质中,与蛋白质之间的相互作用和细胞内的信号传递过程密切相关。植物中含ＬＲＲ的蛋白主要有类受体蛋白激酶、抗病基因编码的蛋白和多聚半乳糖醛酸酶抑制蛋白等,它们分别在细胞的生长发育、抗病反应等过程中发挥着重要作用,其相似的ＬＲＲ结构为从分子水平上研究这些蛋白的作用机制提供了结构基础。     

植物体细胞胚胎发生受体类蛋白激酶的生物学功能

体细胞胚胎发生受体类蛋白激酶(Somatic embryogenesis receptor-like kinases,SERKs)属于膜富亮氨酸重复序列受体类蛋白激酶(Leucine-rich repeat sequence receptor-like kinase,LRR-RLK)家族的第二亚类。SERK具有典型的胞外信号受体结构域、跨膜结构域和胞内激酶活性结构域,研究发现SERKs在植物生命活动中承担着多个角色。文章简述了SERKs的典型结构域特征,重点介绍该类蛋白在体细胞胚发生、生殖发育、激素感应和病理反应方面发挥的功能,同时对该蛋白激酶的研究价值和应用前景进行了探讨。     

苔藓NAC基因家族的生物信息学分析

NAC (NAM, ATAF, CUC)转录因子家族仅存在于陆生植物中,在植物发育、响应胁迫以及生物合成过程中发挥重要作用。许多NAC家族成员的功能已被确定(主要在模式植物中),但在苔藓等早期陆生植物中NAC家族的进化过程尚不清楚。本研究从藓类的小立碗藓(Physcomitrella patens)和泥炭藓(Sphagnum fallax)、苔类的地钱(Marchantia polymorpha)和角苔类的角苔(Anthoceros angustus)中,共鉴定出97个NAC基因,并对其进行NAC转录因子家族进化分析。藓类有大约40个NAC基因,地钱和角苔中只有大约10个NAC基因。在苔藓植物中,NAC基因家族可分为5个亚家族。基因结构和保守结构域分析表明,在同一个亚家族中,大多数NAC基因具有相似的基因结构和编码相似的蛋白基序。共线性分析表明NAC-Ⅱ基因位于藓类植物保守共线性区,并随着藓类植物的整个基因重复事件而扩张。上述研究结果表明NAC基因的扩张不仅发生在维管植物中,也发生在苔藓植物中,这对NAC基因家族的功能扩展是至关重要的。进一步研究结果显示,NAC基因家族的扩增时间与藓类...     

植物体细胞胚胎发生受体类蛋白激酶的生物学功能

体细胞胚胎发生受体类蛋白激酶(Somatic embryogenesis receptor-like kinases, SERKs)属于膜富亮氨酸重复序列受体类蛋白激酶(Leucine-rich repeat sequence receptor-like kinase, LRR-RLK)家族的第二亚类。SERK具有典型的胞外信号受体结构域、跨膜结构域和胞内激酶活性结构域, 研究发现SERKs在植物生命活动中承担着多个角色。文章简述了SERKs的典型结构域特征, 重点介绍该类蛋白在体细胞胚发生、生殖发育、激素感应和病理反应方面发挥的功能, 同时对该蛋白激酶的研究价值和应用前景进行了探讨。     

动物组织蛋白酶L-like基因家族的进化分析

目的:组织蛋白酶L-like家族是在溶酶体中发现的一类非常重要的半胱氨酸组织蛋白酶。其主要功能为催化各种蛋白质的水解,并通过水解蛋白质参与到许多的生理调节过程当中。根据序列比对分析和传统的功能分类,在动物中,组织蛋白酶L-like家族成员包括组织蛋白酶L、V、S、K、H和F。但是这些家族成员之间的进化关系仍然没有详细研究分析清楚。本课题主要研究组织蛋白酶L-like家族成员之间的进化关系。方法:本研究通过搜集整理22个物种的177条组织蛋白酶L-like家族蛋白的序列,并构建系统发育进化树来分析组织蛋白酶L-like家族各成员之间的进化关系。结果:序列数据结果显示,串联重复在组织蛋白酶L-like家族的进化过程中发生。斑马鱼的组织蛋白酶L,爪蟾的组织蛋白酶S和K,大鼠和小鼠的组织蛋白酶L都发生过明显的串联重复事件。进化树结果显示了组织蛋白酶H、S和K、L和V之间的进化关系,组织蛋白酶S和K在脊椎动物出现的进化过程中,从组织蛋白酶L中分化出来,与他们在脊椎动物体内的特异性功能,以及脊椎动物在进化过程中分化产生的特异性功能相对应。结论:在物种进化的过程中,组织蛋白酶L-like家族成员F、H、S和K、L和V按时间顺序分化,这表明组织蛋白酶L-like基因家族结构和功能的分化与新的物种和新的功能出现密切相关。     

植物NLR基因的表达调控及应用策略

含有一个核酸结合位点以及富含亮氨酸重复序列(nucleotide-binding leucine rich repeats,NLR)类抗性基因在植物免疫中发挥重要作用。该文综述了近年来植物NLR基因的结构和功能特点,在转录、转录后、翻译水平的表达调控,植物NLR基因在增强作物抗性中的应用策略方面的研究进展。植物NLR基因表达调控的研究有助于揭示其分子作用机制,增加对NLR基因信号传导过程的了解;植物NLR基因应用策略的研究在开发抗性作物新品种中有较强的应用价值。     

动物组织蛋白酶L=like基因家族的进化分析

目的：组织蛋白酶L-like家族是在溶酶体中发现的一类非常重要的半胱氨酸组织蛋白酶。其主要功能为催化各种蛋白质的水解,并通过水解蛋白质参与到许多的生理调节过程当中。根据序列比对分析和传统的功能分类,在动物中,组织蛋白酶L．1ike家族成员包括组织蛋白酶L、V、S、K、H和F。但是这些家族成员之间的进化关系仍然没有详细研究分析清楚。本课题主要研究组织蛋白酶L-like家族成员之间的进化关系。方法：本研究通过搜集整理22个物种的177条组织蛋白酶L-1ike家族蛋白的序列,并构建系统发育进化树来分析组织蛋白酶L-like家族各成员之间的进化关系。结果：序列数据结果显示,串联重复在组织蛋白酶L-1ike家族的进化过程中发生。斑马鱼的组织蛋白酶L,爪蟾的组织蛋白酶S和K,大鼠和小鼠的组织蛋白酶L都发生过明显的串联重复事件。进化树结果显示了组织蛋白酶H、S和K、L和V之间的进化关系,组织蛋白酶S和K在脊椎动物出现的进化过程中,从组织蛋白酶L中分化出来,与他们在脊椎动物体内的特异性功能,以及脊椎动物在进化过程中分化产生的特异性功能相对应。结论：在物种进化的过程中,组织蛋白酶L-1ike家族成员F、H、S和K、L和V按时间顺序分化,这表明组织蛋白酶L-1ike基因家族结构和功能的分化与新的物种和新的功能出现密切相关。     

Evolutionary dynamics of leucine-rich repeat receptor-like kinases and related genes in plants：A phylogenomic approach

Leucine-rich repeat （LRR） receptor-like kinases （RLKs）, evolutionarily related LRR receptor-like proteins （RLPs） and receptor-like cytoplasmic kinases （RLCKs） have important roles in plant signaling, and their gene subfamilies are large with a complicated history of gene duplication and loss. In three pairs of closely related lineages, including Arabidopsis thaliana and A. lyrata （Arabidopsis）, Lotus japonicus, and Medicago truncatula （Legumes）, Oryza sativa ssp. japonica, and O. sativa ssp. indica （Rice）, we find that LRR RLKs comprise the largest group of these LRR-related subfamilies, while the related RLCKs represent the smal est group. In addition, comparison of orthologs indicates a high frequency of reciprocal gene loss of the LRR RLK/LRR RLP/RLCK subfamilies. Furthermore, pairwise comparisons show that reciprocal gene loss is often associated with lineage-specific duplication（s） in the alternative lineage. Last, analysis of genes in A. thaliana involved in development revealed that most are highly conserved orthologs without species-specific duplication in the two Arabidopsis species and originated from older Arabidopsis-specific or rosid-specific duplications. We discuss＆amp;nbsp;potential pitfal s related to functional prediction for genes that have undergone frequent turnover （duplications, losses, and domain architecture changes）, and conclude that prediction based on phylogenetic relationships wil likely outperform that based on sequence similarity alone.     

Degree of Functional Divergence in Duplicates Is Associated with Distinct Roles in Plant Evolution

Gene duplication is a major mechanism to create new genes. After gene duplication, some duplicated genes undergo functionalization, whereas others largely maintain redundant functions. Duplicated genes comprise various degrees of functional diversification in plants. However, the evolutionary fate of high and low diversified duplicates is unclear at genomic scale. To infer high and low diversified duplicates in Arabidopsis thaliana genome, we generated a prediction method for predicting whether a pair of duplicate genes was subjected to high or low diversification based on the phenotypes of knock-out mutants. Among 4,017 pairs of recently duplicated A. thaliana genes, 1,052 and 600 are high and low diversified duplicate pairs, respectively. The predictions were validated based on the phenotypes of generated knock-down transgenic plants. We determined that the high diversified duplicates resulting from tandem duplications tend to have lineage-specific functions, whereas the low diversified duplicates produced by whole-genome duplications are related to essential signaling pathways. To assess the evolutionary impact of high and low diversified duplicates in closely related species, we compared the retention rates and selection pressures on the orthologs of A. thaliana duplicates in two closely related species. Interestingly, high diversified duplicates resulting from tandem duplications tend to be retained in multiple lineages under positive selection. Low diversified duplicates by whole-genome duplications tend to be retained in multiple lineages under purifying selection. Taken together, the functional diversities determined by different duplication mechanisms had distinct effects on plant evolution.     

Homologs of the Genes for Receptor-Like Kinase Proteins Conferring Plant Resistance to Pathogens: Resistance Gene Homologs in Solanum Species

Direct amplification of the genomic DNA from cultivated and wild Solanum species was used to synthesize three groups of NBS-LRR homologs of the genes which encode the pathogen-recognizing receptor-like serine/threonine kinases (RLK): (1) the NBS-kinase regions homologous to the arabidopsis RPS2 gene, the tobacco N gene, and the flax L6 gene (the corresponding GenBank accession nos. U14158, U15605, and U27081); (2) full-size sequences homologous to the Pto gene of Lycopersicon pimpinellifolium (AF220602); and (3) LRR regions homologous to potato genesGpa2/Rx1 (AJ249449 and AJ011801) and the tomato gene Mi1 (AF091048). The nucleotide and deduced amino acid sequences of the cloned fragments of the genes and pseudogenes were compared to the already known genes and their homologs within the family Solanaceae.     

Evolution of eukaryotic genome architecture: Insights from the study of a rapidly evolving metazoan, Oikopleura dioica: Non-adaptive forces such as elevated mutation rates may influence the evolution of genome architecture

Recent sequencing of the metazoan Oikopleura dioica genome has provided important insights, which challenges the current understanding of eukaryotic genome evolution. Many genomic features of O. dioica show deviation from the commonly observed trends in other eukaryotic genomes. For instance, O. dioica has a rapidly evolving, highly compact genome with a divergent intron-exon organization. Additionally, O. dioica lacks the minor spliceosome and key DNA repair pathway genes. Even with a compact genome, O. dioica contains tandem repeats, comparable to other eukaryotes, and shows lineage-specific expansion of certain protein domains. Here, we review its genomic features in the context of current knowledge, discuss implications for contemporary biology and identify areas for further research. Analysis of the O. dioica genome suggests that non-adaptive forces such as elevated mutation rates might influence the evolution of genome architecture. The knowledge of unique genomic features and splicing mechanisms in O. dioica may be exploited for synthetic biology applications, such as generation of orthogonal splicing systems.     

Self/nonself perception and recognition mechanisms in plants: a comparison of self-incompatibility and innate immunity

Analyses of emerging concepts indicate that parallels exist between self-incompatibility and pathogen recognition. In the case of surveillance of 'nonself', plant immune responses are triggered either by pattern recognition receptors (PRRs) that detect conserved pathogen-associated molecular patterns (PAMPs) or by resistance (R) proteins recognizing isolate-specific pathogen effectors. PAMP detection is an important component of innate immunity in plants and serves as an early warning system for the presence of potential pathogens and activation of plant defense mechanisms. In the Brassicaceae, the recognition of 'self' and self-incompatibility are components of a receptor-ligand based mechanism that utilizes an S receptor kinase (SRK) to perceive and reject 'self'-pollen. SRK is an S-domain receptor-like kinase (RLK), which in turn is part of the RLK family, some members of which represent PRRs involved in the detection of PAMPs. S-domain RLKs also occur in species that do not exhibit self-incompatibility and are up-regulated in response to wounding, PAMPs and pathogen recognition. Although evolution may have driven expansion of certain RLK families to serve roles in particular physiological processes, this may not exclude these receptor types from functioning in different programs. Recent findings on self/nonself recognition are reviewed and conceptual and mechanistic links between microbial recognition and self-incompatibility are discussed.     

神经系统中富亮氨酸重复序列跨膜蛋白的功能研究进展

富亮氨酸重复序列(leucine-rich repeat, LRR)是一种常见的蛋白质结构域．含有富亮氨酸重复序列的蛋白质简称LRR蛋白．LRR蛋白在真核生物和原核生物的细胞和组织中广泛分布,其定位的特异性以及与之相互作用蛋白质的复杂性,决定了LRR蛋白功能的多样性．许多LRR蛋白相对特异性表达于神经系统,绝大多数在神经系统中高表达的LRR蛋白属于跨膜蛋白,它们主要作为细胞黏附分子或配体结合蛋白参与突触的形成、神经突起的生长发育、神经递质的转移和释放等神经系统正常生理活动．LRR蛋白的异常表达将会导致神经、精神系统疾病的发生．     

Rapid migration in gel filtration of the Cf-4 and Cf-9 resistance proteins is an intrinsic property of Cf proteins and not because of their association with high-molecular-weight proteins

Gel filtration is frequently used to study the behaviour and composition of protein complexes. In previous studies, gel filtration analysis of solubilised membranes containing the tomato Cf-4 and Cf-9 resistance proteins indicated that these Cf proteins are present in an approximately 400- and 420-kDa protein complex, respectively, which contains only one Cf molecule per complex, does not contain Rho-related proteins, and does not alter in size upon elicitation. Here, we show that inactive Cf-4 and Cf-9 mutant proteins have a similar large apparent size upon gel filtration analysis. The size remains unaltered after pre-treating the samples under harsh conditions, such as boiling with SDS and incubation in 6 m urea. A similar large apparent size was found for Cf-4 and Cf-9 isolated from SDS gel and for Cf-9 expressed by insect cells. Therefore, the large apparent size observed in our studies appears to be an intrinsic property of the Cf proteins, rather than being caused by association with high-molecular-weight protein(s). Taken together, these results suggest that caution should be taken when interpreting data obtained from gel filtration of LRR-containing proteins.