Genome-wide analysis of basic/helix-loop-helix gene family in peanut and assessment of its roles in pod development

<div><p>The basic/helix-loop-helix (bHLH) proteins constitute a superfamily of transcription factors that are known to play a range of regulatory roles in eukaryotes. Over the past few decades, many bHLH family genes have been well-characterized in model plants, such as <i>Arabidopsis</i>, rice and tomato. However, the bHLH protein family in peanuts has not yet been systematically identified and characterized. Here, 132 and 129 bHLH proteins were identified from two wild ancestral diploid subgenomes of cultivated tetraploid peanuts, <i>Arachis duranensis</i> (AA) and <i>Arachis ipaensis</i> (BB), respectively. Phylogenetic analysis indicated that these <i>bHLH</i>s could be classified into 19 subfamilies. Distribution mapping results showed that peanut <i>bHLH</i> genes were randomly and unevenly distributed within the 10 AA chromosomes and 10 BB chromosomes. In addition, 120 <i>bHLH</i> gene pairs between the AA-subgenome and BB-subgenome were found to be orthologous and 101 of these pairs were highly syntenic in AA and BB chromosomes. Furthermore, we confirmed that 184 <i>bHLH</i> genes expressed in different tissues, 22 of which exhibited tissue-specific expression. Meanwhile, we identified 61 <i>bHLH</i> genes that may be potentially involved in peanut-specific subterranean. Our comprehensive genomic analysis provides a foundation for future functional dissection and understanding of the regulatory mechanisms of bHLH transcription factors in peanuts.</p></div

The chromosomal location and identification of orthologous genes between AA-subgenome and BB-subgenome.

<p>The chromosomal location and identification of orthologous genes between AA-subgenome and BB-subgenome.</p

The distribution of introns within domains of peanut bHLH proteins.

<p>All patterns are color coded and defined as I to X. Introns are indicated by triangles and numbered (1 to 3) based on those present in the bHLH region of Aradu.QV5DJ (shown at the top). The numbers of proteins with each pattern is given at the right.</p

Relative expression analyses of four pod development-related <i>bHLH</i> genes and two <i>PIF</i>s by qRT-PCR among different tissues and different developmental stages of pod.

<p>(A) Expression analysis of pod development-related <i>bHLH</i> genes. (B) Expression analysis of peanut PIF genes. The levels in the roots were arbitrarily set to 1. Error bars represent the standard deviations of three biological replicates.</p

Sequence motif of the bHLH domain in peanut as determined by MEME.

<p>Sequence motif of the bHLH domain in peanut as determined by MEME.</p

Phylogenetic tree constructed by the neighbor-joining method using bHLH domains in peanut, indicating the predicted DNA-binding activities and the intron distribution patterns.

<p>The phylogenetic tree was constructed using MEGA 7.0. The numbers are bootstrap values are based on 1,000 iterations. Only bootstrap values with greater than 50% support are indicated. Roman numerals correspond to the intron patterns as shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0181843#pone.0181843.g003" target="_blank">Fig 3</a>. The different shape on the left side of SlbHLH represents the predicted DNA-binding activity of each protein.</p

Clustering and differential expression analysis of peanut pod development-related <i>bHLH</i> genes among 22 tissues, representing the full development of peanut.

<p>In the heat map, the RPKM values were transformed to log2 (value + 1). The color scale is shown at the right and higher expression levels are shown in red.</p

Information on the consensus motif and conserved amino acid sequences in the bHLH domain.

<p>Information on the consensus motif and conserved amino acid sequences in the bHLH domain.</p

Statistical analysis of DNA-binding characteristics based on the bHLH domain in peanut.

<p>Statistical analysis of DNA-binding characteristics based on the bHLH domain in peanut.</p

Structure–Activity Relationship Study of Rakicidins: Overcoming Chronic Myeloid Leukemia Resistance to Imatinib with 4‑Methylester-Rakicidin A

Natural product rakicidin A induces cell death in TKI-resistant chronic myelogenous leukemia (CML) cells. Therefore, 14 rakicidin A analogues were synthesized via a highly efficient combinatorial strategy and were evaluated against CML cell lines. The conjugated diene moiety was found to be crucial for the anti-CML activity of rakicidin A, and the changes in the configuration(s) at C-2, C-3, C-14, C-15, and C-16 resulted in lower levels of anti-CML activity. The most promising compound was 4-methylester rakicidin A (<b>1a</b>). Compared with rakicidin A, <b>1a</b> exhibited 2.8-fold greater potency against the imatinib-resistant cell line K562/G⁺ and approximately 100-fold enhanced potency compared with that of imatinib. Furthermore, compound <b>1a</b> demonstrated a significantly lower resistance index against Ba/F3 cells expressing BCR-ABL^T315I than bosutinib, dasatinib, nilotinib, and ponatinib, while <b>1a</b> exhibited less effect on normal hematopoietic cells. Preliminary results indicated that <b>1a</b> down-regulated caspase-3 and PARP, which contributes to its K562 cell inhibitory activity