Over-expression of the BnVIT-L2 gene improves the lateral root development and biofortification under iron stress.

The vacuolar iron transporter (VIT) family is responsible for absorbing and storing iron ions in vacuoles. Here, the BnVIT-L2 gene from Brassica napus has been cloned for the first time and was found to be expressed in multiple tissues and organs, induced by iron stress. The BnVIT-L2 protein is located in vacuolar membranes and has the ability to bind both iron and other bivalent metal ions. Over-expression of the BnVIT-L2 gene increased lateral root number and main root length, as well as chlorophyll and iron content in transgenic Arabidopsis plants (BnVIT-L2/At) exposed to iron stress, compared to wild type Col-0. Furthermore, over-expression of this gene improved the adaptability of transgenic B. napus plants (BnVIT-L2-OE) under iron stress. The regulation of plant tolerance under iron stress by BnVIT-L2 gene may involve in the signal of reactive oxygen species (ROS), as suggested by Ribosome profiling sequencing (Ribo-seq). This study provides a reference for investigating plant growth and biofortification under iron stress through the BnVIT-L2 gene.

Identification and molecular evolution of the La and LARP genes in 16 plant species: A focus on the Gossypium hirsutum.

La and La-related proteins (LARPs) are RNA-binding proteins regulating gene expression. Here, identification and molecular evolution of La and LARP gene family were performed in 16 plant species. Firstly, 188 La and LARP genes were identified. Based on phylogenetic tree and gene structure, they can be divided into three categories: La, LARP1 and LARP6. LARP1 can be further divided into LARP1-L and LARP1-S sub-categories. Compared with the LARP1-S, one additional DM15 domain was found in the C-terminal of LARP1-L. La and LARP genes are mainly distributed at both ends of chromosomes with a relatively consistent distribution position in A and D genomes of Gossypium hirsutum. Las and LARPs of G. hirsutum probably came from cruciferae, and gene recombination and chromosome structure variation occurred in G. hirsutum during evolution. The expression patterns and the distribution of cis-acting elements were also analyzed. The results showed that Las and LARPs respond to some abiotic stresses and hormone stimulation. The protein interaction network indicated that La and LARP proteins may be involved in meristem differentiation, hormone signal transduction, and post-translational modification. This study will provide a basis for the further functional and evolutional study of this gene family.

The plant specific SHORT INTERNODES/STYLISH (SHI/STY) proteins: Structure and functions.

Plant specific SHORT INTERNODES/STYLISH (SHI/STY) protein is a transcription factor involved in the formation and development of early lateral organs in plants. However, research on the SHI/STY protein family is not focused enough. In this article, we review recent studies on SHI/STY genes and explore the evolution and structure of SHI/STY. The biological functions of SHI/STYs are discussed in detail in this review, and the application of each biological function to modern agriculture is discussed. All SHI/STY proteins contain typical conserved RING-like zinc finger domain and IGGH domain. SHI/STYs are involved in the formation and development of lateral root, stem extension, leaf morphogenesis, and root nodule development. They are also involved in the regulation of pistil and stamen development and flowering time. At the same time, the regulation of some GA, JA, and auxin signals also involves these family proteins. For each aspect, unanswered or poorly understood questions were identified to help define future research areas. This review will provide a basis for further functional study of this gene family.

AT-HOOK MOTIF NUCLEAR LOCALIZED (AHL) proteins of ancient origin radiate new functions.

AHL (AT-HOOK MOTIF NUCLEAR LOCALIZED) protein is an important transcription factor in plants that regulates a wide range of biological process. It is considered to have evolved from an independent PPC domain in prokaryotes to a complete protein in modern plants. AT-hook motif and PPC conserved domains are the main functional domains of AHL. Since the discovery of AHL, their evolution and function have been continuously studied. The AHL gene family has been identified in multiple species and the functions of several members of the gene family have been studied. Here, we summarize the evolution and structural characteristics of AHL genes, and emphasize their biological functions. This review will provide a basis for further functional study and crop breeding.

Molecular evolutionary analysis of the SHI/STY gene family in land plants: A focus on the Brassica species.

The plant-specific SHORT INTERNODES/STYLISH (SHI/STY) proteins belong to a family of transcription factors that are involved in the formation and development of early lateral roots. However, the molecular evolution of this family is rarely reported. Here, a total of 195 SHI/STY genes were identified in 21 terrestrial plants, and the Brassica species is the focus of our research. Their physicochemical properties, chromosome location and duplication, motif distribution, exon-intron structures, genetic evolution, and expression patterns were systematically analyzed. These genes are divided into four clades (Clade 1/2/3/4) based on phylogenetic analysis. Motif distribution and gene structure are similar in each clade. SHI/STY proteins are localized in the nucleus by the prediction of subcellular localization. Collinearity analysis indicates that the SHI/STYs are relatively conserved in evolution. Whole-genome duplication is the main factor for their expansion. SHI/STYs have undergone intense purifying selection, but several positive selection sites are also identified. Most promoters of SHI/STY genes contain different types of cis-elements, such as light, stress, and hormone-responsive elements, suggesting that they may be involved in many biological processes. Protein-protein interaction predicted some important SHI/STY interacting proteins, such as LPAT4, MBOATs, PPR, and UBQ3. In addition, the RNA-seq and qRT-PCR analysis were studied in detail in rape. As a result, SHI/STYs are highly expressed in root and bud, and can be affected by Sclerotinia sclerotiorum, drought, cold, and heat stresses. Moreover, quantitative real-time PCR (qRT-PCR) analyses indicates that expression levels of BnSHI/STYs are significantly altered in different treatments (cold, salt, drought, IAA, auxin; ABA, abscisic acid; 6-BA, cytokinin). It provides a new understanding of the evolution and expansion of the SHI/STY family in land plants and lays a foundation for further research on their functions.

Insights Into the Molecular Evolution of AT-Hook Motif Nuclear Localization Genes in Brassica napus.

AT-hook motif nuclear localization (AHL) proteins belong to a family of transcription factors, and play important roles in plant growth and development and response to various stresses through protein-DNA and protein-protein interactions. To better understand the Brassica napus AHL gene family, AHL genes in B. napus and related species were analyzed. Using Arabidopsis as a reference, 122 AHL gene family members were first identified in B. napus. According to the phylogenetic tree and gene organization, the BnaAHLs were classified into two clades (Clade-A and Clade-B) and three types (Type-I, Type-II, and Type-III). Gene organization and motif distribution analysis suggested that the AHL gene family is relatively conserved during evolution. These BnaAHLs are unevenly distributed on 38 chromosomes and expanded by whole-genome duplication (WGD) or segmental duplication. And large-scale loss events have also occurred in evolution. All types of BnaAHLs are subject to purification or neutral selection, while some positive selection sites are also identified in Type-II and Type-III groups. At the same time, the purification effect of Type-I members are stronger than that of the others. In addition, RNA-seq data and cis-acting element analysis also suggested that the BnaAHLs play important roles in B. napus growth and development, as well as in response to some abiotic and biotic stresses. Protein-protein interaction analysis identified some important BnaAHL-binding proteins, which also play key roles in plant growth and development. This study is helpful to fully understand the origin and evolution of the AHL gene in B. napus, and lays the foundation for their functional studies.

Characterization and molecular evolution of claudin genes in the Pungitius sinensis.

Claudins are a family of integrated membrane-bound proteins involving in paracellular tightness, barrier forming, ion permeability, and substrate selection at tight junctions of chordate epithelial and endothelial cells. Here, 39 putative claudin genes were identified in the Pungitius sinensis based on the high throughput RNA-seq. Conservative motif distribution in each group suggested functional relevance. Divergence of duplicated genes implied the species' adaptation to the environment. In addition, selective pressure analyses identified one site, which may accelerate functional divergence in this protein family. Pesticides cause environmental pollution and have a serious impact on aquatic organisms when entering the water. The expression pattern of most claudin genes was affected by organophosphorus pesticide, indicating that they may be involved in the immune regulation of organisms and the detoxification of xenobiotics. Protein-protein network analyses also exhibited 439 interactions, which implied the functional diversity. It will provide some references for the functional study on claudin genes.

Molecular Evolution and Characterization of Fish Stathmin Genes.

Stathmin is a highly conserved microtubule remodeling protein, involved in many biological processes such as signal transduction, cell proliferation, neurogenesis and so on. However, little evolutional information has been reported about this gene family in fish. In this study, 175 stathmin genes were identified in 27 species of fish. Conserved exon-intron structure and motif distributions were found in each group. Divergence of duplicated genes implied the species' adaptation to the environment. Functional divergence suggested that the evolution of stathmin is mainly influenced by purifying selection, and some residues may undergo positive selection. Moreover, synteny relationship near the stathmin locus was relatively conserved in some fish. Network analyses also exhibited 74 interactions, implying functional diversity. The expression pattern of some stathmin genes was also investigated under pesticide stress. These will provide useful references for their functional research in the future.

Transcriptome-Based Identification and Molecular Evolution of the Cytochrome P450 Genes and Expression Profiling under Dimethoate Treatment in Amur Stickleback (Pungitius sinensis).

Cytochrome P450s (CYPs) are a family of membrane-bound mono-oxygenase proteins, which are involved in cell metabolism and detoxification of various xenobiotic substances. In this study, we identified 58 putative CYP genes in Amur stickleback (Pungitius sinensis) based on the transcriptome sequencing. Conserved motif distribution suggested their functional relevance within each group. Some present recombination events have accelerated the evolution of this gene family. Moreover, a few positive selection sites were identified, which may have accelerated the functional divergence of this family of proteins. Expression patterns of these CYP genes were investigated and indicated that most were affected by dimethoate treatment, suggesting that CYPs were involved in the detoxication of dimethoate. This study will provide a foundation for the further functional investigation of CYP genes in fishes.