ORGAN BOUNDARIES Domain Gene Family Research Articles

Identification of the lateral organ boundary domain gene family and its preservation by exogenous salicylic acid in Cerasus humilis.

The online version contains supplementary material available at 10.1007/s12298-024-01438-5.

Genome-Wide Analysis of Soybean Lateral Organ Boundaries Domain Gene Family Reveals the Role in Phytophthora Root and Stem Rot

The plant-specific lateral organ boundaries (LOB) domain (LBD) proteins, a family of transcription factors, play important roles in plant growth and development, as well as in responses to various stresses. However, little is known about the functions of LBD genes in soybean (Glycine max). In this study, we investigated the evolution and classification of the LBD family in soybean by a phylogenetic tree of the LBD gene family from 16 species. Phylogenetic analysis categorized these proteins into two classes (Class I and Class II) with seven subgroups. Moreover, we found that all the 18 LBD ancestors in angiosperm were kept in soybean, common bean genomes, and genome-wide duplication, suggesting the main force for the expansion of LBD from common bean to soybean. Analysis of gene expression profiling data indicated that 16 GmLBD genes were significantly induced at different time points after inoculation of soybean plants (cv. Huachun 6) with Phytophthora sojae (P. sojae). We further assessed the role of four highly upregulated genes, GmLBD9, GmLBD16, GmLBD23, and GmLBD88, in plant defense in soybean hairy roots using the transient overexpression and knockdown assays. The results showed that GmLBD9 and GmLBD23 negatively regulate plant immunity against P. sojae, whereas GmLBD16 and GmLBD88 positively manipulate plant immunity against P. sojae. Collectively, our findings expand our knowledge of the origin and evolution of the GmLBD gene family in soybean and promote the potential application of these genes in soybean genetic improvement.

Genome-wide identification and characterization of the lateral organ boundaries domain gene family in Brassica rapa var. rapa

The Lateral Organ Boundaries Domain (LBD) genes encode highly conserved plant-specific LOB domain proteins which regulate growth and development in various species. However, members of the LBD gene family have yet to be identified in Brassica rapa var. rapa. In the present study, fifty-nine LBD genes were identified and distributed on 10 chromosomes. The BrrLBD proteins are predicted to encode hydrophobic polypeptides between 118 and 394 amino acids in length and with molecular weights ranging from 13.31 to 44.24 kDa; the theoretical pI for these proteins varies from 4.83 to 9.68. There were 17 paralogous gene pairs in the BrrLBD family, suggesting that the amplification of the BrrLBD gene family involved large-scale gene duplication events. Members of the BrrLBD family were divided into 7 subclades (class I a to e, class II a and b). Analysis of gene structure and conserved domains revealed that most BrrLBD genes of the same subclade had similar gene structures and protein motifs. The expression profiles of 59 BrrLBD genes were determined through Quantitative Real-time fluorescent PCR (qRT-PCR). Most BrrLBD genes in the same subclade had similar gene expression profiles. However, the expression patterns of 7 genes differed from their duplicates, indicating that although the gene function of most BrrLBD genes has been conserved, some BrrLBD genes may have undergone evolutionary change.

The LATERAL ORGAN BOUNDARIES Domain gene family in grapevine: genome-wide characterization and expression analyses during developmental processes and stress responses

LATERAL ORGAN BOUNDARIES (LOB) DOMAIN (LBD) constitute a family of plant-specific transcription factors with key roles in the regulation of plant organ development, pollen development, plant regeneration, pathogen response, and anthocyanin and nitrogen metabolisms. However, the role of LBDs in fruit ripening and in grapevine (Vitis vinifera L.) development and stress responses is poorly documented. By performing a model curation of LBDs in the latest genome annotation 50 genes were identified. Phylogenetic analysis showed that LBD genes can be grouped into two classes mapping on 16 out of the 19 V. vinifera chromosomes. New gene subclasses were identified that have not been characterized in other species. Segmental and tandem duplications contributed significantly to the expansion and evolution of the LBD gene family in grapevine as noticed for other species. The analysis of cis-regulatory elements and transcription factor binding sites in the VviLBD promoter regions suggests the involvement of several hormones in the regulation of LBDs expression. Expression profiling suggest the involvement of LBD transcription factors in grapevine development, berry ripening and stress responses. Altogether this study provides valuable information and robust candidate genes for future functional analysis aiming to clarify mechanisms responsible for the onset of fruit ripening and fruit defense strategies.

Genomewide analysis of the lateral organ boundaries domain gene family in Eucalyptus grandis reveals members that differentially impact secondary growth.

SummaryLateral Organ Boundaries Domain (LBD) proteins are plant‐specific transcription factors playing crucial roles in growth and development. However, the function of LBD proteins in Eucalyptus grandis remains largely unexplored. In this study, LBD genes in E. grandis were identified and characterized using bioinformatics approaches. Gene expression patterns in various tissues and the transcriptional responses of EgLBDs to exogenous hormones were determined by qRT‐PCR. Functions of the selected EgLBDs were studied by ectopically overexpressing in a hybrid poplar (Populus alba × Populus glandulosa). Expression levels of genes in the transgenic plants were investigated by RNA‐seq. Our results showed that there were forty‐six EgLBD members in the E. grandis genome and three EgLBDs displayed xylem‐ (EgLBD29) or phloem‐preferential expression (EgLBD22 and EgLBD37). Confocal microscopy indicated that EgLBD22, EgLBD 29 and EgLBD37 were localized to the nucleus. Furthermore, we found that EgLBD22, EgLBD29 and EgLBD37 were responsive to the treatments of indol‐3‐acetic acid and gibberellic acid. More importantly, we demonstrated EgLBDs exerted different influences on secondary growth. Namely, 35S::EgLBD37 led to significantly increased secondary xylem, 35S::EgLBD29 led to greatly increased phloem fibre production, and 35S::EgLBD22 showed no obvious effects. We revealed that key genes related to gibberellin, ethylene and auxin signalling pathway as well as cell expansion were significantly up‐ or down‐regulated in transgenic plants. Our new findings suggest that LBD genes in E. grandis play important roles in secondary growth. This provides new mechanisms to increase wood or fibre production.

ASYMMETRIC LEAVES2-LIKE15 gene, a member of AS2/LOB family, shows a dual abaxializing or adaxializing function in Arabidopsis lateral organs

In determining leaf adaxial fates, Arabidopsis ASYMMERTIC LEAVES1 (AS1) and AS2/LBD6 are essential. The Arabidopsis ASYMMETRIC LEAVES2-LIKE15/LBD17 gene, one member of the LATERAL ORGAN BOUNDARY DOMAIN gene family, is expressed at the base of juvenile lateral roots, as well as in boundaries between meristems and organ primordial. For better comprehending the function of ASL15/LBD17 in the Arabidopsis development, its antisense-expression construct was constructed, and some 35S:ASL15/LBD17 transgenic plants that were antisense overexpression mutants were attained. The transgenic plants can specify either abaxial or adaxial cell fate in differently shaped rosette leaves. In detail, slightly and extremely narrow rosette leaves (class I) displayed abaxial cell traits, compared with those of Col-0. Inflorescence stems of these transgenic plants also showed abaxial organ identity. Both radial needle-like and filamentous symmetric rosette leaves (class II) presented adaxial cell fate, in contrast to those of wild type (Col-0). However, in the background of AS2 mutation, antisense 35S:ASL15 only presented abaxial organ identity, implying that the influences of antisense 35:ASL15 require a functional AS2 gene. In addition, antisense 35S:ASL15 was defective in proximodistal patterning. In addition, antisense 35S:ASL15 lead to the enhancement of the transcript levels of the KNOX genes, i.e., KNAT2, KNAT6, and STM, but not of the related KNAT1 gene. Taken together, our findings show that ASL15/LBD17 has a dual abaxializing or adaxializing function, and is also related to distal and proximal patterning in the lateral organs of Arabidopsis. Therefore, ASL15/LBD17 has multiple functions in the Arabidopsis development.

Genomewide analysis of the lateral organ boundaries domain gene family in Vitis vinifera.

In plants, the transcription factor families have been implicated in many important biological processes. These processes include morphogenesis, signal transduction and environmental stress responses. Proteins containing the lateral organ boundaries domain (LBD), which encodes a zinc finger-like domain are only found in plants. This finding indicates that this unique gene family regulates only plant-specific biological processes. LBD genes play crucial roles in the growth and development of plants such as Arabidopsis, Oryza sativa, Zea mays, poplar, apple and tomato. However, relatively little is known about the LBD genes in grape (Vitis vinifera). In this study, we identified 40 LBD genes in the grape genome. A complete overview of the chromosomal locations, phylogenetic relationships, structures and expression profiles of this gene family during development in grape is presented here. Phylogenetic analysis showed that the LBD genes could be divided into classes I and II, together with LBDs from Arabidopsis. We mapped the 40 LBD genes on the grape chromosomes (chr1-chr19) and found that 37 of the predicted grape LBD genes were distributed in different densities across 12 chromosomes. Grape LBDs were found to share a similar intron/exon structure and gene length within the same class. The expression profiles of grape LBD genes at different developmental stages were analysed using microarray data. Results showed that 21 grape LBD genes may be involved in grape developmental processes, including preveraison, veraison and ripening. Finally, we analysed the expression patterns of six LBD genes through quantitative real-time polymerase chain reation analysis. The six LBD genes showed differential expression patterns among the three representative grape tissues, and five of these genes were found to be involved in responses to mannitol, sodium chloride, heat stress and low temperature treatments. To our knowledge, this is the first study to analyse the LBD gene family in grape and provides valuable information for classification and functional investigation of this gene family.

Genomewide analysis of LATERAL ORGAN BOUNDARIES Domain gene family in Zea mays.

The investigation of transcription factor (TF) families is a major focus of postgenomic research. The plant-specific ASYMMETRIC LEAVES2-LIKE (ASL) / LATERAL ORGAN BOUNDARIES Domain (LBD) proteins constitute a major zincfinger-like-domain transcription factor family, and regulate diverse biological processes in plants. However, little is known about LBD genes in maize (Zea mays). In this study, a total of 44 LBD genes were identified in maize genome and were phylogenetically clustered into two groups (I and II), together with LBDs from Arabidopsis. The predicted maize LBDs were distributed across all the 10 chromosomes with different densities. In addition, the gene structures of maize LBDs were analysed. The expression profiles of the maize LBD genes under normal growth conditions were analysed by microarray data and qRT-PCR. The results indicated that LBDs might be involved in various aspects of physiological and developmental processes in maize. To our knowledge, this is the first report of a genomewide analysis of the maize LBD gene family, which would provide valuable information for understanding the classification and putative functions of the gene family.

Modification of flowers and leaves in Cockscomb (Celosia cristata) ectopically expressing Arabidopsis ASYMMERTIC LEAVES2-LIKE38 (ASL38/LBD41) gene

ASYMMERTIC LEAVES2-LIKE38 (ASL38/LBD41), isolated from Arabidopsis, is a member of the LATERAL ORGAN BOUNDARY DOMAIN gene family. We reported that ASL38 might be involved in the dorsoventral determination in extremely folded or crinkly leaves of 35S:ASL38.cockscomb plants; suggesting ASL38 is a transcript factor, and regulates a number of genes that are involved in the morphogenesis and development of plants. To verify this speculation, in this work, we constructed the binary vector pBI121–pMD-18T, which contained the GFP and coding sequences of ASL38, and introduced them into cockscomb via Agrobacterium tumefaciens. We found that ASL38-GFP fusion protein was localized in discrete subnuclear bodies, indicating ASL38 might be a nuclear protein and function as a transcription factor. In modification of flowering plants, many potentially useful genes that are involved in the pathways associated with flower and plant morphology have been cloned. Transcription factors regulating plant development and biosynthetic or regulatory genes involved in plant hormones are common candidates. If 35S:ASL38 cockscomb plants are altered in morphology, these morphological modifications could pave the foundation for the selection of novel flower varieties. As it was speculated by us, in this work, we showed that these 35S:ASL38 cockscomb flowered earlier and their flowers were turned into multiple column patterns, when compared with wild-type cockscomb. Moreover, leaves of some 35S:ASL38 plants revealed lobed and dissected patterns, and extremely, two leaf blades were developed on the same petiole; which was never found in wild-type cockscomb. Together, these morphological modifications of cockscomb indicate that we have successfully attained some novel lines of cockscombs. These lines can have potential practical applications.

JLO regulates embryo patterning and organ initiation by controlling auxin transport

In Arabidopsis, lateral organ initiation correlates with the formation of an auxin maximum in a group of cells at the periphery of the shoot apical meristem (SAM). This signal establishes founder cells that build the lateral organ. Primordia initiation is closely associated with the creation of a functional boundary that separates the newly formed primordium from the remainder of the meristem. In the June issue of Plant Cell, we have characterised the JLO (for Jagged Lateral Organ) gene of Arabidopsis, a member of the Lateral Organ boundary Domain gene family. JLO is expressed in boundaries and regulates both auxin transport, via a negative regulation of PIN auxin export carriers, and meristem fate by promoting the expression of the KNOX genes SHOOTMERISTEMLESS (STM) and BP/KNAT1. In this Addendum, we discuss the regulation of PIN genes by JLO, and propose a model for JLO function during embryonic and post-embryonic development.

Arabidopsis JAGGED LATERAL ORGANSIs Expressed in Boundaries and CoordinatesKNOXandPINActivity

Plant lateral organs are initiated as small protrusions on the flanks of shoot apical meristems. Organ primordia are separated from the remainder of the meristem by distinct cell types that create a morphological boundary. The Arabidopsis thaliana gain-of-function mutant jagged lateral organs-D (jlo-D) develops strongly lobed leaves, indicative of KNOX gene misexpression, and the shoot apical meristem arrests organ initiation prematurely, terminating in a pin-like structure. The JLO gene, a member of the LATERAL ORGAN BOUNDARY DOMAIN gene family, is expressed in boundaries between meristems and organ primordia and during embryogenesis. Inducible JLO misexpression activates expression of the KNOX genes SHOOT MERISTEMLESS and KNAT1 in leaves and downregulates the expression of PIN auxin export facilitators. Consequently, bulk auxin transport through the inflorescence stem is drastically reduced. During embryogenesis, JLO is required for the initiation of cotyledons and development beyond the globular stage. Converting JLO into a transcriptional repressor causes organ fusions, showing that during postembryonic development, JLO function is required to maintain the integrity of boundaries between cell groups with indeterminate or determinate fates.

Comparison and evolution analysis of two rice subspecies LATERAL ORGAN BOUNDARIES domain gene family and their evolutionary characterization from Arabidopsis

The plant specific LATERAL ORGAN BOUNDARIES (LOB) domain (LBD) gene family has a potential role in lateral organ development. Thirty-five LBD genes in a japonica rice (Nipponbare) (designated OsJLBD) and in an indica rice (9311) (designated OsILBD) were identified based on the current databases of the two rice subspecies. A new rice LBD gene with two LOB domains and two predicted coiled coil structures in both subspecies was found, which is not found in other plant species based on the current NCBI Genbank database. OsJLBD and OsILBD genes have similar chromosomal distribution pattern. Both OsJLBD and OsILBD genes can be divided into 7 subclasses (classes Ia–e, II and III (see Table 1)) and no subclass-specific expression pattern was observed. No introns have been predicted in all class Ie genes in both OsJLBD and OsILBD subfamilies. The genome and tandem duplication has contributed to the neofunctionalization and formation of new rice subclasses, but the mechanism of diploidization and limited tandem duplication have contributed to fewer LBD genes in rice than in Arabidopsis. Functional studies of genes in subclasses may help to determine whether special sequence structure (intron–exon, spacing characters of motifs) has caused special expression pattern of subclasses.