Most studies of crop salinity tolerance are conducted under short-term stress condition within one growth stage. Understanding of the mechanisms of crop response to long-term salinity stress (LSS) is valuable for achieving the improvement of crop salinity tolerance. In the current study, we exposed allohexaploid wheat seeds to LSS conditions from germination stage to young seedling stage for 30 days. To elucidate the adaptive strategy of allohexaploid wheat to LSS, we analyzed chloroplast ultrastructure, leaf anatomy, transcriptomic profiling and concentrations of plant hormones and organic compatible solutes, comparing stressed and control plants.Transcriptomic profiling and biochemical analysis showed that energy partitioning between general metabolism maintenance and stress response may be crucial for survival of allohexaploid wheat under LSS. Under LSS, wheat appeared to shift energy from general maintenance to stress response through stimulating the abscisic acid (ABA) pathway and suppressing gibberellin and jasmonic acid pathways in the leaf. We further distinguished the expression status of the A, B, and D homeologs of any gene triad, and also surveyed the effects of LSS on homeolog expression bias for salinity-tolerant triads. We found that LSS had similar effects on expression of the three homeologs for most salinity-tolerant triads. However, in some of these triads, LSS induced different effects on the expression of the three homeologs.The shift of the energy from general maintenance to stress response may be important for wheat LSS tolerance. LSS influences homeolog expression bias of salinity-tolerant triads.

研究黑果枸杞在不同浓度盐胁迫下基因表达谱变化情况,为进一步研究黑果枸杞抗盐分子机制奠定研究基础。对0（CK）、50、250 mmol/L NaCl溶液胁迫的黑果枸杞组培苗的根和叶在胁迫时间为0、1、12 h时分别取样,采用转录组测序（RNA-Seq）技术进行测序分析。结果表明,转录组测序共产生 222.49 Gb 原始数据,拼接出 Unigenes 86 037条,注释到 7大功能数据库（GO、KEGG、KOG、NR、Pfam、Swiss-Prot和egg NOG）上的 Unigenes 总数为46 594个,占总Unigenes 的54.76%,还有38 929个Unigenes在这些数据库中没有得到注释。通过 GO 分类和 KEGG Pathway 富集性分析,分别归于 51 个 GO 类别和 211条代谢途径。差异表达基因分析显示,黑果枸杞叶片和根的上调基因和下调基因数随着NaCl浓度的增大和处理时间的延长均呈增加趋势,叶片中的上调基因数（7 514）小于下调基因数（9 032）,根中的上调基因数（12 347）大于下调基因数（11 559）。在黑果枸杞盐胁迫下转录组中发现28 325个SSR位点,最多的为单核苷酸 SSR,占 70.47%。综合分析表明,黑果枸杞对盐胁迫的反应是一个多基因参与、多个生物过程协同调控的过程,基因表达量的变化可能是基因调控的主要方式。

The basic helix-loop-helix (bHLH) transcription factor family is one of the largest transcription factor gene families in Arabidopsis thaliana, and contains a bHLH motif that is highly conserved throughout eukaryotic organisms. Members of this family have two conserved motifs, a basic DNA binding region and a helix-loop-helix (HLH) region. These proteins containing bHLH domain usually act as homo- or heterodimers to regulate the expression of their target genes, which are involved in many physiological processes and have a broad range of functions in biosynthesis, metabolism and transduction of plant hormones. Although there are a number of articles on different aspects to provide detailed information on this family in plants, an overall summary is not available. In this review, we summarize various aspects of related studies that provide an overview of insights into the pleiotropic regulatory roles of these transcription factors in plant growth and development, stress response, biochemical functions and the web of signaling networks. We then provide an overview of the functional profile of the bHLH family and the regulatory mechanisms of other proteins.

bHLH (basic helix-loop-helix)是植物中一个重要的转录因子家族, 在调控植物生长发育、逆境胁迫及信号转导过程中发挥着重要作用。目前, 动物中大部分bHLH转录因子功能已明确, 但是在植物中, 尤其是玉米中的研究报道较少。在前期工作中, 我们对玉米生长发育过程中的4个关键时期进行了根系表型鉴定和转录组测序分析, 发现转录因子ZmbHLH91在六叶期(V6)、十二叶期(V12)和抽雄期(VT)的相邻时期间的表达均差异显著, 且ZmbHLH91在V6, V12和VT这些根系生长发育活跃期的表达量较高, 推测该基因可能调控玉米根系的生长发育。为探究ZmbHLH91基因在根系生长和抵抗逆境胁迫方面的作用, 本研究克隆了ZmbHLH91 (AC: NC_AQL05369)基因, 该基因全长2112 bp, 具有bHLH转录因子家族特有的保守结构域。实时荧光定量PCR (RT-qPCR)分析表明, ZmbHLH91在玉米根中的表达量最高, 其在三叶期幼根中的表达量高于抽雄期成熟根。在高盐、渗透、低温以及脱水胁迫处理下, 玉米幼苗中ZmbHLH91的表达均上调。在无胁迫处理的1/2 MS培养基上, ZmbHLH91异源表达拟南芥与野生型拟南芥的根长无明显差别, 而在梯度浓度NaCl和甘露醇处理的培养基上, ZmbHLH91异源表达拟南芥的根均长于野生型, 且差异显著; 在土壤中进行干旱和高盐处理后, 转基因拟南芥比野生型拟南芥表现出更好的生长状态、更高的过氧化物酶(POD)活性和更高的绿叶率。推测ZmbHLH91基因可能参与响应高盐、干旱以及渗透胁迫等逆境条件。ZmbHLH91基因在茉莉酸(jasmonic acid, JA)、脱落酸(abscisic acid, ABA)等激素处理下均上调表达, 推测ZmbHLH91基因可能参与响应JA和ABA激素信号。在梯度浓度JA处理的培养基上, 转基因拟南芥的根长均长于野生型, 且差异显著。酵母双杂交实验表明ZmbHLH91与ZmMYC2相互作用, ZmMYC2是JA信号通路中重要的蛋白, 由此推测ZmbHLH91蛋白可能参与JA信号通路。综上所述, ZmbHLH91可能参与高盐、干旱和渗透胁迫应答及JA信号转导途径。本研究为进一步解析ZmbHLH91在玉米中的生物学功能提供了重要的参考依据。

Although bHLH transcription factors play important roles regulating plant development and abiotic stress response and tolerance, few functional studies have been performed in wheat. In this study, we isolated and characterized a bHLH gene, TabHLH39, from wheat. The TabHLH39 gene is located on wheat chromosome 5DL, and the protein localized to the nucleus and activated transcription. TabHLH39 showed variable expression in roots, stems, leaves, glumes, pistils and stamens and was induced by polyethylene glycol, salt and cold treatments. Further analysis revealed that TabHLH39 overexpression in Arabidopsis significantly enhanced tolerance to drought, salt and freezing stress during the seedling stage, which was also demonstrated by enhanced abiotic stress-response gene expression and changes to several physiological indices. Therefore, TabHLH39 has potential in transgenic breeding applications to improve abiotic stress tolerance in crops.Copyright © 2016 Elsevier Inc. All rights reserved.

Basic helix-loop-helix protein (bHLH) is the most extensive class of transcription factors in eukaryotes, which can regulate gene expression through interaction with specific motif in target genes. bHLH transcription factor is not only universally involved in plant growth and metabolism, including photomorphogenesis, light signal transduction and secondary metabolism, but also plays an important role in plant response to stress. In this review, we discuss the role of bHLH in plants in response to stresses such as drought, salt and cold stress. To provide a strong evidence for the important role of bHLH in plant stress response, in order to provide new ideas and targets for the prevention and treatment of plant stress resistance.Copyright © 2018 Elsevier Inc. All rights reserved.

The basic/helix-loop-helix (bHLH) proteins are a superfamily of transcription factors that bind as dimers to specific DNA target sites and that have been well characterized in nonplant eukaryotes as important regulatory components in diverse biological processes. Based on evidence that the bHLH protein PIF3 is a direct phytochrome reaction partner in the photoreceptor's signaling network, we have undertaken a comprehensive computational analysis of the Arabidopsis genome sequence databases to define the scope and features of the bHLH family. Using a set of criteria derived from a previously defined consensus motif, we identified 147 bHLH protein–encoding genes, making this one of the largest transcription factor families in Arabidopsis. Phylogenetic analysis of the bHLH domain sequences permits classification of these genes into 21 subfamilies. The evolutionary and potential functional relationships implied by this analysis are supported by other criteria, including the chromosomal distribution of these genes relative to duplicated genome segments, the conservation of variant exon/intron structural patterns, and the predicted DNA binding activities within subfamilies. Considerable diversity in DNA binding site specificity among family members is predicted, and marked divergence in protein sequence outside of the conserved bHLH domain is observed. Together with the established propensity of bHLH factors to engage in varying degrees of homodimerization and heterodimerization, these observations suggest that the Arabidopsis bHLH proteins have the potential to participate in an extensive set of combinatorial interactions, endowing them with the capacity to be involved in the regulation of a multiplicity of transcriptional programs. We provide evidence from yeast two-hybrid and in vitro binding assays that two related phytochrome-interacting members in the Arabidopsis family, PIF3 and PIF4, can form both homodimers and heterodimers and that all three dimeric configurations can bind specifically to the G-box DNA sequence motif CACGTG. These data are consistent, in principle, with the operation of this combinatorial mechanism in Arabidopsis.

Basic helix-loop-helix proteins (bHLHs) are found throughout the three eukaryotic kingdoms and constitute one of the largest families of transcription factors. A growing number of bHLH proteins have been functionally characterized in plants. However, some of these have not been previously classified. We present here an updated and comprehensive classification of the bHLHs encoded by the whole sequenced genomes of Arabidopsis (Arabidopsis thaliana), Populus trichocarpa, Oryza sativa, Physcomitrella patens, and five algae species. We define a plant bHLH consensus motif, which allowed the identification of novel highly diverged atypical bHLHs. Using yeast two-hybrid assays, we confirm that (1) a highly diverged bHLH has retained protein interaction activity and (2) the two most conserved positions in the consensus play an essential role in dimerization. Phylogenetic analysis permitted classification of the 638 bHLH genes identified into 32 subfamilies. Evolutionary and functional relationships within subfamilies are supported by intron patterns, predicted DNA-binding motifs, and the architecture of conserved protein motifs. Our analyses reveal the origin and evolutionary diversification of plant bHLHs through differential expansions, domain shuffling, and extensive sequence divergence. At the functional level, this would translate into different subfamilies evolving specific DNA-binding and protein interaction activities as well as differential transcriptional regulatory roles. Our results suggest a role for bHLH proteins in generating plant phenotypic diversity and provide a solid framework for further investigations into the role carried out in the transcriptional regulation of key growth and developmental processes.

利用生物信息学方法，在西瓜测序基因组97103 中共鉴定出96 个bHLH 家族成员，其中有94 个可以被定位到西瓜的11 条染色体上。通过基因结构和结构域序列保守性的预测，发现这些基因的序列长度和内含子数量变化很大，但bHLH 结构域序列比较保守。用拟南芥中39 条已知的bHLH 蛋白序列和西瓜的96 条bHLH 蛋白序列构建系统发育树，结果显示西瓜的bHLH 家族可以进一步被分为11 个亚族。运用荧光定量实时PCR 技术，分析了该家族中21 个基因在西瓜响应非生物胁迫时的表达水平，结果表明，8 个基因受低温胁迫诱导表达，13 个基因受ABA胁迫诱导表达，14 个基因受盐胁迫诱导表达。ClabHLH41在3 种胁迫下表达量均显著增加，说明其在低温、ABA 和盐胁迫应答中可能发挥着重要作用。