植物NAC转录因子的研究进展

NAC转录因子是特异存在于植物中的具有多种生物功能的新型转录因子.其家族成员N端含有保守NAC结构域(约150个氨基酸),C端为高度变异的转录激活区.NAC基因表达特异,功能涉及植物生长发育、激素调控和胁迫响应等重要方面.现综述植物NAC转录因子的基本结构、生物功能及新型膜相关转录因子的研究.     

The intracellular distal tail of the Na+/H+ exchanger NHE1 is intrinsically disordered: implications for NHE1 trafficking

Intrinsic disorder is important for protein regulation, yet its role in regulation of ion transport proteins is essentially uninvestigated. The ubiquitous plasma membrane carrier protein Na(+)/H(+) Exchanger isoform 1 (NHE1) plays pivotal roles in cellular pH and volume homeostasis, and its dysfunction is implicated in several clinically important diseases. This study shows, for the first time for any carrier protein, that the distal part of the C-terminal intracellular tail (the cdt, residues V686-Q815) from human (h) NHE1 is intrinsically disordered. Further, we experimentally demonstrated the presence of a similar region of intrinsic disorder (ID) in NHE1 from the teleost fish Pleuronectes americanus (paNHE1), and bioinformatic analysis suggested ID to be conserved in the NHE1 family. The sequential variation in structure propensity as determined by NMR, but not the amplitude, was largely conserved between the h- and paNHE1cdt. This suggests that both proteins contain molecular recognition features (MoRFs), i.e., local, transiently formed structures within an ID region. The functional relevance of the most conserved MoRF was investigated by introducing a point mutation that significantly disrupted the putative binding feature. When this mutant NHE1 was expressed in full length NHE1 in AP1 cells, it exhibited impaired trafficking to the plasma membrane. This study demonstrated that the distal regulatory domain of NHE1 is intrinsically disordered yet contains conserved regions of transient structure. We suggest that normal NHE1 function depends on a protein recognition element within the ID region that may be linked to NHE1 trafficking via an acidic ER export motif.     

互花米草NAC转录因子家族的鉴定与表达分析

互花米草(Spartina alterniflora)作为一种海岸带盐生植物,高度耐盐胁迫,但因为缺少参考基因组,其耐盐的分子机制却尚未见报道。NAC家族蛋白是植物特有的转录因子,调控植物的生长发育和胁迫应答。为了鉴定互花米草NAC蛋白(SaNAC)并探究它们与互花米草生长发育及胁迫响应之间的关系,本研究以互花米草三代全长转录组数据为参考,通过与水稻(Oryza sativa)、拟南芥(Arabidopsis thaliana)和玉米(Zea mays)NAC蛋白序列进行比对,并结合保守功能域进一步筛选,最终找到62个SaNAC蛋白。从蛋白序列比对、进化、motif预测、同源性比较、亚细胞定位、组织表达以及非生物胁迫下的基因差异表达等方面分别对互花米草NAC家族成员进行分析,结果发现SaNAC蛋白均含有保守的NAM结构域,且在进化上与水稻NAC家族具有一定的相似性;SaNAC家族中的两个蛋白SaNAC9和SaNAC49在细胞核表达;另外,本研究还发现互花米草SaNAC基因表达具有高度组织和胁迫应答差异性。这些结果表明互花米草NAC转录因子家族不仅具有保守的功能域,而且在调控互花米草的生长发育和非生物胁迫响应过程中具有重要的作用。     

植物NAC转录因子的结构功能及其表达调控研究进展

NAC转录因子是近十年来新发现的具有多种生物功能的植物特异转录因子。该家族转录因子的共同特点是其N端为保守的大约150个氨基酸的NAC结构域,C端为高度变异的转录调控区。它们在植物生长发育、激素调节和抵抗逆境等方面发挥着重要的作用。本文主要就植物NAC转录因子的基本结构特征、生物学功能、表达调控及其最新研究进展进行综述。     

Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling

Regulation, recognition and cell signaling involve the coordinated actions of many players. To achieve this coordination, each participant must have a valid identification (ID) that is easily recognized by the others. For proteins, these IDs are often within intrinsically disordered (also ID) regions. The functions of a set of well-characterized ID regions from a diversity of proteins are presented herein to support this view. These examples include both more recently described signaling proteins, such as p53, alpha-synuclein, HMGA, the Rieske protein, estrogen receptor alpha, chaperones, GCN4, Arf, Hdm2, FlgM, measles virus nucleoprotein, RNase E, glycogen synthase kinase 3beta, p21(Waf1/Cip1/Sdi1), caldesmon, calmodulin, BRCA1 and several other intriguing proteins, as well as historical prototypes for signaling, regulation, control and molecular recognition, such as the lac repressor, the voltage gated potassium channel, RNA polymerase and the S15 peptide associating with the RNA polymerase S-protein. The frequent occurrence and the common use of ID regions in important protein functions raise the possibility that the relationship between amino acid sequence, disordered ensemble and function might be the dominant paradigm for the molecular recognition that serves as the basis for signaling and regulation by protein molecules.     

Interactions via intrinsically disordered regions: what kind of motifs?

Proteins containing intrinsically disordered (ID) regions are widespread in eukaryotic organisms and are mostly utilized in regulatory processes. ID regions can mediate binary interactions of proteins or promote organization of large assemblies. Post-translational modifications of ID regions often serve as decision points in signaling pathways. Why Nature distinguished ID proteins in molecular recognition functions? In a simple view, binding of ID regions is accompanied by a large entropic penalty as compared to folded proteins. Even in complexes however, ID regions can preserve their conformational freedom, thereby recruit further partners and perform various functions. What sort of benefits ID regions offer for molecular interactions and which properties are exploited in the corresponding complexes? Here, we review models explaining the recognition mechanisms of ID proteins. Motif-based interactions are central to all proposed scenarios, including prestructured elements, anchoring sites and linear motifs. We aim to extract consensus features of the models, which could be used to predict ID-binding sites for a variety of partners.     

GRAB proteins,novel members of the NAC domain family,isolated by their interaction with a geminivirus protein

Geminiviruses encode a few proteins and depend on cellular factors to complete their replicative cycle. As a way to understand geminivirus-host interactions, we have searched for cellular proteins which interact with viral proteins. By using the yeast two-hybrid technology and the wheat dwarf geminivirus (WDV) RepA protein as a bait, we have isolated a family of proteins which we termed GRAB (for Geminivirus Rep A-binding). We report here the molecular characterization of two members, GRAB1 and GRAB2. We have found that the 37 C-terminal amino acids of RepA are required for interaction with GRAB proteins. This region contains residues conserved in an equivalent region of the RepA proteins encoded by other viruses of the WDV subgroup. The N-terminal domain of GRAB proteins is necessary and sufficient to interact with WDV RepA. GRAB proteins contain an unique acidic C-terminal domain while their N-terminal domain, of ca. 170 amino acids, are highly conserved in all of them. Interestingly, this conserved N-terminal domain of GRAB proteins exhibits a significant amino acid homology to the NAC domain present in proteins involved in plant development and senescence. GRAB1 and GRAB2 mRNAs are present in cultured cells and roots but are barely detectable in leaves. GRAB expression inhibits WDV DNA replication in cultured wheat cells. Our studies highlight the importance that the pathway(s) mediated by GRAB proteins, as well as by other NAC domain-containing proteins, might have on geminivirus DNA replication in connection to plant growth, development and senescence pathways.     

An integrated approach to the analysis and modeling of protein sequences and structures. III. A comparative study of sequence conservation in protein structural families using multiple structural alignments

The information required to generate a protein structure is contained in its amino acid sequence, but how three-dimensional information is mapped onto a linear sequence is still incompletely understood. Multiple structure alignments of similar protein structures have been used to investigate conserved sequence features but contradictory results have been obtained, due, in large part, to the absence of subjective criteria to be used in the construction of sequence profiles and in the quantitative comparison of alignment results. Here, we report a new procedure for multiple structure alignment and use it to construct structure-based sequence profiles for similar proteins. The definition of "similar" is based on the structural alignment procedure and on the protein structural distance (PSD) described in paper I of this series, which offers an objective measure for protein structure relationships. Our approach is tested in two well-studied groups of proteins; serine proteases and Ig-like proteins. It is demonstrated that the quality of a sequence profile generated by a multiple structure alignment is quite sensitive to the PSD used as a threshold for the inclusion of proteins in the alignment. Specifically, if the proteins included in the aligned set are too distant in structure from one another, there will be a dilution of information and patterns that are relevant to a subset of the proteins are likely to be lost.In order to understand better how the same three-dimensional information can be encoded in seemingly unrelated sequences, structure-based sequence profiles are constructed for subsets of proteins belonging to nine superfolds. We identify patterns of relatively conserved residues in each subset of proteins. It is demonstrated that the most conserved residues are generally located in the regions where tertiary interactions occur and that are relatively conserved in structure. Nevertheless, the conservation patterns are relatively weak in all cases studied, indicating that structure-determining factors that do not require a particular sequential arrangement of amino acids, such as secondary structure propensities and hydrophobic interactions, are important in encoding protein fold information. In general, we find that similar structures can fold without having a set of highly conserved residue clusters or a well-conserved sequence profile; indeed, in some cases there is no apparent conservation pattern common to structures with the same fold. Thus, when a group of proteins exhibits a common and well-defined sequence pattern, it is more likely that these sequences have a close evolutionary relationship rather than the similarities having arisen from the structural requirements of a given fold.     

植物NAC转录因子

植物生命过程依赖众多转录因子去调控基因的表达。NAC类蛋白是近十多年来新发现的一类植物特有的、数量较多的转录因子家族。研究发现,拥有一个介导DNA结合的特有的N末端新转录因子折叠结构域和一个具有高度多样性的C端转录功能区是这类转录因子共同的结构特征。NAC转录因子不仅普遍参与了植物生长发育过程的调控,包括茎顶端分生组织、花器官的发育、侧根的形成、细胞次生壁的形成以及叶片衰老等,还参与了胁迫应答、激素调控以及诱导寄主对病原菌侵染产生抗性等过程。本文综述了植物NAC转录因子的结构特征、生物学功能、作用机理以及表达调控等方面的研究进展,对该领域的研究进行了展望。     

Structure of the retinal determination protein Dachshund reveals a DNA binding motif

The Dachshund proteins are essential components of a regulatory network controlling cell fate determination. They have been implicated in eye, limb, brain, and muscle development. These proteins cannot be assigned to any recognizable structural or functional class based on amino acid sequence analysis. The 1.65 A crystal structure of the most conserved domain of human DACHSHUND is reported here. The protein forms an alpha/beta structure containing a DNA binding motif similar to that found in the winged helix/forkhead subgroup of the helix-turn-helix family. This unexpected finding alters the previously proposed molecular models for the role of Dachshund in the eye determination pathway. Furthermore, it provides a rational framework for future mechanistic analyses of the Dachshund proteins in several developmental contexts.