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.

The effect of cropping system on the distribution of organic carbon (OC) and nitrogen (N) in soil aggregates has not been well addressed, which is important for understanding the sequestration of OC and N in agricultural soils. We analyzed the distribution of OC and N associated with soil aggregates in three unfertilized cropping systems in a 27-year field experiment: continuously cropped alfalfa, continuously cropped wheat and a legume-grain rotation. The objectives were to understand the effect of cropping system on the distribution of OC and N in aggregates and to examine the relationships between the changes in OC and N stocks in total soils and in aggregates. The cropping systems increased the stocks of OC and N in total soils (0–40 cm) at mean rates of 15.6 g OC m^-2 yr^-1 and 1.2 g N m^-2 yr^-1 relative to a fallow control. The continuous cropping of alfalfa produced the largest increases at the 0–20 cm depth. The OC and N stocks in total soils were significantly correlated with the changes in the >0.053 mm aggregates. 27-year of cropping increased OC stocks in the >0.053 mm size class of aggregates and N stocks in the >0.25 mm size class but decreased OC stocks in the <0.053 mm size class and N stocks in the 0.25 mm aggregate size class accounted for more than 97% of the total increases in the continuous wheat and the legume-grain rotation systems. These results suggested that long-term cropping has the potential to sequester OC and N in soils and that the increases in soil OC and N stocks were mainly due to increases associated with aggregates >0.053 mm.

Cyclophilin 38 (CYP38) plays a crucial role in the assembly and stability of photosystem II (PSII), but its molecular mechanism remains unclear. In this study, we identified thylakoid lumen protein 7.6 (TLP7.6) as an in vivo interactor of CYP38. Under normal growth conditions, the tlp7.6 single mutant exhibited no significant phenotypic differences compared to wild-type Col-0. However, the cyp38-2/tlp7.6-1 double mutant displayed severe developmental defects, including stunted growth, delayed flowering, yellowish leaf, short primary roots, abnormal chloroplast ultrastructure, and reduced biomass, which were more pronounced than those in either the tlp7.6 or cyp38-2 single mutant. Photosynthetic analysis revealed that PSII capacities in cyp38-2/tlp7.6-1 and cyp38-2 mutants were significantly reduced, consistent with their slow-growth phenotype. Blue native PAGE analysis demonstrated a substantial reduction in PSII supercomplexes and light-harvesting complex II (LHCII) in cyp38-2/tlp7.6-1, while PSII monomer (PSII-M) were significantly increased. Immunoblotting and two-dimensional gel electrophoresis further confirmed decreased levels of key components of PSII, PSI, and ATPase subunits in the double mutant. Altogether, these results highlight the role of TLP7.6 as an assistive factor in CYP38-mediated PSII assembly, and provide insights into thylakoid lumen protein function in photosynthesis.

BHLH proteins regulate plant development, hormone responses, and stress adaptation; however, the precise functions of most bHLHs remain unclear. In this study, we explored the functions and mechanism of a bHLH gene, IBH1-LIKE 1 (IBL1), in Arabidopsis. IBL1 negatively controlled root growth, hypocotyl elongation, and leaf expansion, as indicated by larger or longer cells in ibl1 compared with Col-0 in the early vegetative process. IBL1 promoted photomorphogenesis and participated in various hormone pathways. In later vegetative stages, ibl1 plants were smaller and weaker than Col-0. During the reproductive stage, the deficiency of IBL1 led to earlier bolting and unhealthy shoots but did not obviously impair gametogenesis and embryogenesis. Longer pistils occurred in ibl1 plants, while stamens exhibited normal length, indicating that IBL1 restricted pistil cell elongation. The unsynchronized sexual organs led to substantial incomplete pollination and vacant seats in siliques. Transcriptomic analysis implied that IBL1 functions via affecting the expression of cell expansion-related genes. Yeast two-hybrid, bimolecular fluorescence complementation, in vitro protein pull-down, electrophoretic mobility shift assays, and dual luciferase assays indicated that IBL1 interacts with other bHLHs, including PRE5, HBI1, and CIL2. These bHLH proteins could constitute a tri-antagonistic system to regulate plant cell elongation/expansion. In a proposed model, IBL1 and PRE5 antagonistically regulate the activity of HBI1/CIL2 to control target gene expression and eventually fine-tune cell elongation/expansion. This study reveals physiological roles and the working mode of IBL1 and provides insights into the regulation of plant growth and development.