SBP-box Genes Research Articles

Identification and expression analysis of the SQUAMOSA promoter-binding protein (SBP)-box gene family in Prunus mume.

SQUAMOSA promoter-binding protein (SBP)-box family genes encode plant-specific transcription factors that play crucial roles in plant development, especially flower and fruit development. However, little information on this gene family is available for Prunus mume, an ornamental and fruit tree widely cultivated in East Asia. To explore the evolution of SBP-box genes in Prunus and explore their functions in flower and fruit development, we performed a genome-wide analysis of the SBP-box gene family in P. mume. Fifteen SBP-box genes were identified, and 11 of them contained an miR156 target site. Phylogenetic and comprehensive bioinformatics analyses revealed that different groups of SBP-box genes have undergone different evolutionary processes and varied in their length, structure, and motif composition. Purifying selection has been the main selective constraint on both paralogous and orthologous SBP-box genes. In addition, the sequences of orthologous SBP-box genes did not diverge widely after the split of P. mume and Prunus persica. Expression analysis of P. mume SBP-box genes revealed their diverse spatiotemporal expression patterns. Three duplicated SBP-box genes may have undergone subfunctionalization in Prunus. Most of the SBP-box genes showed high transcript levels in flower buds and young fruit. The four miR156-nontargeted genes were upregulated during fruit ripening. Together, these results provide information about the evolution of SBP-box genes in Prunus. The expression analysis lays the foundation for further research on the functions of SBP-box genes in P. mume and other Prunus species, especially during flower and fruit development.

Cloning of tae-MIR156 precursor gene and sequence polymorphisms of tae-miR156 targeted TaSPL17

Squamosa-promoter binding protein (SBP)-box genes, encoding plant-specific transcription factors, play an important role in plant development. Some members of the SBP-box gene family are regulated by miR156. In this study, we cloned the tae-MIR156 precursor gene, which could form a stem loop after its transcription. Sequence analysis showed that TaSPL3 and TaSPL17 had putative targets of tae-miR156 among the ten wheat SBP-box genes. The diploid donor species of hexaploid common wheat (Triticum aestivum, genome AABBDD), i.e., Triticum urartu (AA) UR209 and Aegilops speltoides Y2001 (SS, closely related to BB) possessed more than one copy of SPL17 (SPL17-A1, SPL17-A2 and SPL17-A3 from Triticum urartu; SPL17-B1, SPL17-B2 and SPL17-B3 from Aegilops speltoides), while Aegilops tauschii (DD) Ae38 only possessed one (SPL17-D). The identities between nucleotide sequences of SPL17-A2 and SPL17-B2, SPL17-A3 and SPL17-B3 or SPL17-D were higher than 99%. They were highly similar with the sequence of TaSPL17 in common wheat cultivars Chinese Spring, Hengguan 35 and Shuangfengshou. These genes might originate from a common ancestor and were highly conserved in the process of evolution. The target site of tae-miR156 in TaSPL17 was also highly conserved in two subgroups consisted of accessions with diverse spike number per plant and genetic background.

Molecular Characterization and Expression Analysis of Triticum aestivum Squamosa‐Promoter Binding Protein‐Box Genes Involved in Ear Development

Wheat (Triticum aestivum L.) is one of the most important crops in the world. Squamosa-promoter binding protein (SBP)-box genes play a critical role in regulating flower and fruit development. In this study, 10 novel SBP-box genes (TaSPL genes) were isolated from wheat ((Triticum aestivum L.) cultivar Yanzhan 4110). Phylogenetic analysis classified the TaSPL genes into five groups (G1–G5). The motif combinations and expression patterns of the TaSPL genes varied among the five groups with each having own distinctive characteristics: TaSPL20/21 in G1 and TaSPL17 in G2 mainly expressed in the shoot apical meristem and the young ear, and their expression levels responded to development of the ear; TaSPL6/15 belonging to G3 were upregulated and TaSPL1/23 in G4 were downregulated during grain development; the gene in G5 (TaSPL3) expressed constitutively. Thus, the consistency of the phylogenetic analysis, motif compositions, and expression patterns of the TaSPL genes revealed specific gene structures and functions. On the other hand, the diverse gene structures and different expression patterns suggested that wheat SBP-box genes have a wide range of functions. The results also suggest a potential role for wheat SBP-box genes in ear development. This study provides a significant beginning of functional analysis of SBP-box genes in wheat.

Genome-Wide Identification and Evolutionary Analysis of the SBP-Box Gene Family in Castor Bean

Genes in the SQUAMOSA promoter-binding-protein (SBP-box) gene family encode transcriptional regulators and perform a variety of regulatory functions that involved in the developmental and physiological processes of plants. In this study, a comprehensive computational analysis identified 15 candidates of the SBP-box gene family in the castor bean (Ricinus communis). The phylogenetic and domain analysis indicated that these genes were divided into two groups (group I and II). The group II was a big branch and was further classified into three subgroups (subgroup II-1 to 3) based on the phylogeny, gene structures and conserved motifs. It was observed that the genes of subgroup II-1 had distinct evolutionary features from those of the other two subgroups, however, were more similar to those of group I. Therefore, we inferred that group I and subgroup II-1 might retain ancient signals, whereas the subgroup II-2 and 3 exhibited the divergence during evolutionary process. Estimation of evolutionary parameters (dN and dN/dS) further supported our hypothesis. At first, the group I was more constrained by strong purifying selection and evolved slowly with a lower substitution rate than group II. As regards the three subgroups, subgroup II-1 had the lowest rate of substitution and was under strong purifying selection. By contrast, subgroups II-2 and 3 evolved more rapidly and experienced less purifying selection. These results indicated that the different evolutionary rates and selection strength caused the different evolutionary patterns of the members of SBP-box genes in castor bean. Taken together, these results provide better insights into understanding evolutionary divergence of the members of SBP-box gene family in castor bean and provide a guide for future functional diverse analyses of this gene family.

Genome-wide identification and phylogenetic analysis of the SBP-box gene family in melons.

The SBP-box gene family is specific to plants and encodes a class of zinc finger-containing transcription factors with a broad range of functions. Although SBP-box genes have been identified in numerous plants, including green algae, moss, silver birch, snapdragon, Arabidopsis, rice, and maize, there is little information concerning SBP-box genes, or the corresponding miR156/157, function in melon. Using the highly conserved sequence of the Arabidopsis thaliana SBP-box domain protein as a probe of information sequence, the genome-wide protein database of melon was explored to obtain 13 SBP-box protein sequences, which were further divided into 4 groups, based on phylogenetic analysis. A further analysis centered on the melon SBP-box genetic family's phylogenetic evolution, sequence similarities, gene structure, and miR156 target sequence was also conducted. Analysis of all the expression patterns of melon SBP-box family genes showed that the SBP-box genes were detected in 7 kinds of tissue, and fruit had the highest expression level. CmSBP11 tends to present its specific expression in melon fruit and root. CmSBP09 expression was the highest in flower. Overall, the molecular evolution and expression pattern of the melon SBP-box gene family, revealed by these results, suggest its function differentiation that followed gene duplication.

SPL8 Acts Together with the Brassinosteroid-Signaling Component BIM1 in Controlling Arabidopsis thaliana Male Fertility.

The non-miR156 targeted SBP-box gene SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 8 (SPL8), plays an important role in Arabidopsis anther development, where its loss-of-function results in a semi-sterile phenotype. Fully male-sterile plants are obtained when a spl8 loss-of-function mutation is introduced into a 35S:MIR156 genetic background, thereby revealing functional redundancy between SPL8 and miR156-targeted SBP-box genes. Here, we show that BIM1, a gene encoding a bHLH protein involved in brassinosteroid signaling and embryonic patterning, functions redundantly with SPL8 in its requirement for male fertility. Although bim1 single mutants displayed a mild fertility problem due to shortened filaments in some flowers, mutation of BIM1 significantly enhanced the semi-sterile phenotype of the spl8 mutant. Expression of both SPL8 and BIM1 was detected in overlapping expression domains during early anther developmental stages. Our data suggest that in regulating anther development, SPL8 and BIM1 function cooperatively in a common complex or in synergistic pathways. Phylogenetic analysis supports the idea of an evolutionary conserved function for both genes in angiosperm anther development.

Genome-wide identification and analysis of the SBP-box family genes in apple (Malus × domestica Borkh.)

SQUAMOSA promoter binding protein (SBP)-box genes encode a family of plant-specific transcription factors and play many crucial roles in plant development. In this study, 27 SBP-box gene family members were identified in the apple (Malus×domestica Borkh.) genome, 15 of which were suggested to be putative targets of MdmiR156. Plant SBPs were classified into eight groups according to the phylogenetic analysis of SBP-domain proteins. Gene structure, gene chromosomal location and synteny analyses of MdSBP genes within the apple genome demonstrated that tandem and segmental duplications, as well as whole genome duplications, have likely contributed to the expansion and evolution of the SBP-box gene family in apple. Additionally, synteny analysis between apple and Arabidopsis indicated that several paired homologs of MdSBP and AtSPL genes were located in syntenic genomic regions. Tissue-specific expression analysis of MdSBP genes in apple demonstrated their diversified spatiotemporal expression patterns. Most MdmiR156-targeted MdSBP genes, which had relatively high transcript levels in stems, leaves, apical buds and some floral organs, exhibited a more differential expression pattern than most MdmiR156-nontargeted MdSBP genes. Finally, expression analysis of MdSBP genes in leaves upon various plant hormone treatments showed that many MdSBP genes were responsive to different plant hormones, indicating that MdSBP genes may be involved in responses to hormone signaling during stress or in apple development.

Genomic organization, phylogenetic comparison and differential expression of the SBP-box family genes in grape.

BackgroundThe SBP-box gene family is specific to plants and encodes a class of zinc finger-containing transcription factors with a broad range of functions. Although SBP-box genes have been identified in numerous plants including green algae, moss, silver birch, snapdragon, Arabidopsis, rice and maize, there is little information concerning SBP-box genes, or the corresponding miR156/157, function in grapevine.Methodology/Principal FindingsEighteen SBP-box gene family members were identified in Vitis vinifera, twelve of which bore sequences that were complementary to miRNA156/157. Phylogenetic reconstruction demonstrated that plant SBP-domain proteins could be classified into seven subgroups, with the V. vinifera SBP-domain proteins being more closely related to SBP-domain proteins from dicotyledonous angiosperms than those from monocotyledonous angiosperms. In addition, synteny analysis between grape and Arabidopsis demonstrated that homologs of several grape SBP genes were found in corresponding syntenic blocks of Arabidopsis. Expression analysis of the grape SBP-box genes in various organs and at different stages of fruit development in V. quinquangularis ‘Shang-24’ revealed distinct spatiotemporal patterns. While the majority of the grape SBP-box genes lacking a miR156/157 target site were expressed ubiquitously and constitutively, most genes bearing a miR156/157 target site exhibited distinct expression patterns, possibly due to the inhibitory role of the microRNA. Furthermore, microarray data mining and quantitative real-time RT-PCR analysis identified several grape SBP-box genes that are potentially involved in the defense against biotic and abiotic stresses.ConclusionThe results presented here provide a further understanding of SBP-box gene function in plants, and yields additional insights into the mechanism of stress management in grape, which may have important implications for the future success of this crop.

Virus-induced gene complementation reveals a transcription factor network in modulation of tomato fruit ripening

Plant virus technology, in particular virus-induced gene silencing, is a widely used reverse- and forward-genetics tool in plant functional genomics. However the potential of virus technology to express genes to induce phenotypes or to complement mutants in order to understand the function of plant genes is not well documented. Here we exploit Potato virus X as a tool for virus-induced gene complementation (VIGC). Using VIGC in tomato, we demonstrated that ectopic viral expression of LeMADS-RIN, which encodes a MADS-box transcription factor (TF), resulted in functional complementation of the non-ripening rin mutant phenotype and caused fruits to ripen. Comparative gene expression analysis indicated that LeMADS-RIN up-regulated expression of the SBP-box (SQUAMOSA promoter binding protein-like) gene LeSPL-CNR, but down-regulated the expression of LeHB-1, an HD-Zip homeobox TF gene. Our data support the hypothesis that a transcriptional network may exist among key TFs in the modulation of fruit ripening in tomato.

Exploring the evolutionary differences of SBP-box genes targeted by miR156 and miR529 in plants

The combinatorial control of one target by multiple miRNAs brings big challenges to elucidate its precise evolutionary mechanism. Squamosa promoter binding protein-like (SBP) gene family exhibits the different regulatory patterns, in which some members are only regulated by miR156 and others by miR156 and miR529. Here, we explored the different evolutionary patterns and rates between miR156 targets and miR529 ones in three species (moss, rice, and maize). Our work found that the miR529 targets were members of miR156 target dataset, indicative of cooperative control. Further phylogenetic analyses as well as gene structure features demonstrated that miR529 targets derived from a monophyletic branch of miR156 targets which evolved into two independent branches duo to the ancient gene duplication. Moreover, inspection of evolutionary rate parameters (d(N)/d(S), d(N) and d(S)) for miR156 targets and miR529 ones revealed they were under different selection strength. MiR529 targets were more constraint by strong purifying selection and evolved conservatively with a slow rate. By contrast, miR156 targets evolved more rapidly and experienced more relaxed purifying selection, which may contribute to their functional diversification. Our results will enhance the understanding of different evolutionary fates of SBP-box genes regulated by the different numbers of miRNA families before functional studies.

Overexpression of Arabidopsis miR157b induces bushy architecture and delayed phase transition in Torenia fournieri

miR156/157 is a small RNA molecule that is highly conserved among various plant species. Overexpression of miR156/157 has been reported to induce bushy architecture and delayed phase transition in several plant species. To investigate the effect of miR157 overexpression in a horticultural plant, and to explore the applicability of miRNA to molecular breeding, we introduced Arabidopsis MIR157b (AtMIR157b) into torenia (Torenia fournieri). The resulting 35S:AtMIR157b plants showed a high degree of branching along with small leaves, which resembled miR156/157-overexpressing plants of other species. We also isolated torenia SBP-box genes with target miR156/157 sequences and confirmed that their expression was selectively downregulated in 35S:AtMIR157b plants. The reduced accumulation of mRNA was probably due to sequence specificity. Moreover, expression of torenia homologs of the SBP-box protein-regulated genes TfLFY and TfMIR172 was also reduced by AtmiR157 overexpression. These findings suggest that the molecular mechanisms of miR156/157 regulation are conserved between Arabidopsis and torenia. The bushy architecture and small leaves of 35S:AtMIR157b torenia plants could be applied in molecular breeding of various horticultural plants as well as for increasing biomass and crop production.

Genomic organization, phylogenetic comparison and differential expression of the SBP-box family of transcription factors in tomato

SBP-box genes represent transcription factors ubiquitously found in the plant kingdom and recognized as important regulators of many different aspects of plant development. In this study, 15 SBP-box gene family members were identified in tomato and analyzed with respect to their genomic organization and other structural features. Phylogenetic reconstruction based on the DNA-binding SBP-domain, allowed the classification of the SlySBP proteins into eight groups representing clear orthologous relationships to family members of other flowering plants and the moss Physcomitrella. In order to have a better understanding of their possible function in the development of a fleshy-fruit species like tomato, the mRNA expression levels of all SlySBP genes were quantified in vegetative and reproductive organs of plants, at different stages of growth. As transcripts of ten SlySBP genes were found to carry putative miR156- and miR157-response elements, the expression levels of the corresponding microRNAs were determined as well, revealing different patterns of expression. In addition, eight putative miR156 and four miR157 encoding loci could be identified in the tomato genome, four of them forming a polycistronic cluster. Whereas miR156 and miR157 levels were highest in seedlings, leaves and anthers of young flowers, most miR156-targeted SlySBP genes were found to be expressed in young inflorescences and during fruit development and ripening, suggesting a particularly important role during tomato reproductive growth. The data presented provide a basis for future clarification of the various functions that SBP-box gene family members play in tomato growth and development.

Genome-wide identification, phylogeny, and expression analysis of the SBP-box gene family in grapevine

The SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SBP) proteins form a family of transcriptional regulators, which are present exclusively in plants. Members of this family control processes such as flower development, sporogenesis, toxin resistance, control of GA levels, and response to copper. A genome-wide characterization of this family has not been conducted in a berry species, such as grapevine. Recent publication of the complete grapevine genome opens the possibility for an in depth analysis of the SBP-box gene family in grapevine. By screening the available databases, we identified 19 SBP-box genes with high sequence identity within the conserved SBP domain. An analysis of a complete set of SBP-box proteins in grapevine is presented, including their classification, gene structures, conserved motifs, and phylogenetic relationships. The grapevine SBP-box proteins can be classified into three groups (A, B, and C) based on their phylogenetic relationships with Arabidopsis SBP-box proteins. The expression patterns of the SBP-box genes were further investigated by searching against EST and microarray data. We found that the grapevine SBP-box genes were expressed primarily in flowers and fruit. The comparison of the SBP-box proteins of grapevine and tomato suggested that grapevine SBP-box genes might play an important role in fruit development.

SQUAMOSA-PROMOTER BINDING PROTEIN 1 initiates flowering in Antirrhinum majus through the activation of meristem identity genes

The degree to which developmental genetic pathways are conserved across distantly related organisms is a major question in biology. In Arabidopsis thaliana (L.) Heynh., inflorescence development is initiated in response to a combination of external and internal floral inductive signals that are perceived across the whole plant, but are integrated within the shoot apical meristem. Recently, it was demonstrated that SQUAMOSA-PROMOTER BINDING PROTEIN (SBP)-box proteins regulate A. thaliana flowering time by mediating signals from the autonomous and photoperiod pathways, and by directly activating key genes involved in inflorescence and floral meristem identity, including FRUITFULL (FUL), APETALA1 (AP1) and LEAFY (LFY). In the distantly related core eudicot species Antirrhinum majus L., paralogous SBP-box proteins SBP1 and SBP2 have likewise been implicated in regulating the AP1 ortholog SQUAMOSA (SQUA). To test the hypothesis that SBP-box genes are also involved in the floral induction of A. majus, we used a reverse genetic approach to silence SBP1. SBP1-silenced lines are late to nonflowering, and show reduced apical dominance. Furthermore, expression and sequence analyses suggest that the SBP1-mediated transition to flowering occurs through the positive regulation of FUL/LFY homologs. Together, these data outline the utility of virus-induced gene silencing in A. majus, and provide new insight into the conservation of flowering time genetic pathways across core eudicots.

MicroRNAs and their targets from Arabidopsis to rice: half conserved and half diverged

MicroRNAs are 21to 24-nucleotide long, endogenous non-coding RNAs in eukaryotes (Hannon, 2002). Mature microRNAs generated by Dicer are incorporated into an RNA-induced silencing complex (RISC), resulting in gene silencing via the cleavage of a target mRNA or the repression of target mRNA translation (Qi et al, 2005). Thus, microRNAs play a key role in post-transcriptional gene silencing, and microRNA-based gene silencing pathways are critical in developmental regulation, biotic and abiotic adaptations, and hormone responses in plants (Baulcombe, 2004; Jones-Rhoades et al., 2006). In microRNA-based gene silencing, the microRNAtarget mRNA pair determines the specificity of the biological effect. Hundreds of microRNAs have been identified in plants by cloning and deep genomic sequencing (Griffiths-Jones et al., 2008). Thus, a key step in determining the biological function of a microRNA is to identify its target. However, our knowledge of microRNA targets is incomplete due to limitations imposed by the methods used to identify microRNA targets. Traditionally, microRNA targets have been identified from computational predictions based on sequence matching between a microRNA and its target mRNA (Rhoades et al., 2002). Thus, a new approach is needed to facilitate the identification of microRNA targets on a global scale. Degradome sequencing is a new approach that integrates high-throughput sequencing, experimental approaches, and bioinformatic analyses (German et al., 2009). More than 100 microRNA targets in Arabidopsis have been isolated using this method (Addo-Quaye et al., 2008; German et al., 2008), suggesting that degradome sequencing is a powerful tool for microRNA-target pair identification. The isolation and experimental validation of microRNAtarget pairs from the monocot model plant rice using a degradome sequencing approach was reported in this issue by Dr. Xiaofeng Cao’s group (Zhou et al., 2010). They identified 177 mRNAs that were targeted by 87 unique microRNAs (Zhou et al., 2010). Among them, microRNAs known to be conserved in the plant kingdom targeted about half of the identified target mRNAs, and, interestingly, about 70% of the target mRNAs encoded transcription factors (Zhou et al., 2010). One example is the mi156SBP-box gene mRNA pair (Fig. 1A). The Arabidopsis genome encodes thirteen SBP-box genes (SPLs), ten of which are mi156 targets (Schwab et al., 2005; Wu et al., 2009; Wang et al., 2009). The mi156-SPL pathway regulates the vegetative-phase transition, flowering, leaf initiation, and apical dominance in Arabidopsis (Schwab et al., 2005; Wu et al., 2009; Wang et al., 2009). Consistent with the microRNA-target of the mi156-SPL mRNA pairs in Arabidopsis, eleven SPL mRNAs are mi156 targets in rice (Zhou et al., 2010). These conserved microRNA-target pairs may represent common regulatory nodes for the regulation of fundamental developmental processes and responses to environmental signals in the plant kingdom. The second half of the identified target genes were found to be targeted by non-conserved microRNAs (Zhou et al., 2010). These non-conserved microRNA-target pairs may be involved in riceor grass-specific processes or responses, such as osa-miR528/Os0738290 interaction (Fig. 1B). Interestingly, a large proportion of the nonconserved microRNAs targeted the 5’or 3’-untranslated region of their target mRNAs (Zhou et al., 2010). Thus, these non-conserved microRNAs may regulate gene expression via manners other than mRNA cleavage, and translational repression by microRNAs is more common in rice than in Arabidopsis. Therefore, rice is a better model than Arabidopsis to use in determining the mechanism of microRNA-mediated translational repression in plants. What will be the next step after this useful and much needed atlas of microRNA-target interactions is completed? First, it will be possible to address the biological functions of microRNA-target transcript pairs in rice. The genetic manipulation of microRNA-mRNA pairs in planta Received December 19, 2009; accepted December 23, 2009

Cloning and Expression Analysis of BplSPL2, a Novel SBP-Box Gene from Betula Platyphylla

ABSTRACTA cDNA representing the squamosa promoter binding protein-box genes (SBP-box gene), BplSPL2, containing the full coding sequence was obtained from Betula platyphylla by 5' rapid amplification of cDNA (5'RACE). Sequence analysis showed that BplSPL2 was 925 bp in length with a 525-bp open-reading frame encoding 175 amino acids. By comparing the expression patterns of BplSPL2 and BplSPL1 using quantitative real-time PCR, we determined that the expression of the former is inflorescence- specific and that it is temporally expressed during inflorescence development. Overall, the 2 SBP-box genes exhibit different expression patterns.

Arabidopsis SBP-Box Genes SPL10, SPL11 and SPL2 Control Morphological Change in Association with Shoot Maturation in the Reproductive Phase

Lateral organ traits in higher plants, such as lamina shape and trichome distribution, change gradually in association with shoot maturation. Regulation of this shoot maturation process in the vegetative phase has been extensively investigated, and members of the SQUAMOSA PROMOTER BINDING PROTEIN (SBP)-box family of transcription factors have been shown to be involved in this process. However, little is known about the regulation of shoot maturation in the reproductive phase. We analyzed SPL10, SPL11 and SPL2, which are closely related members of the SBP-box family in Arabidopsis. While cauline leaves had oblong lamina and few trichomes emerged on cauline leaves and flowers in wild-type plants, transgenic plants expressing a dominant repressor version of SPL10/11/2 had wide cauline leaves and many trichomes on their cauline leaves and flowers. These traits were similar to those observed at an earlier reproductive phase in wild-type plants. Loss-of-function mutants for spl10/11/2 showed similar phenotypes, indicating that SPL10, SPL11 and SPL2 redundantly control proper development of lateral organs in association with shoot maturation in the reproductive phase. In the vegetative phase, lamina shape was affected in SPL10 transgenic plants, while trichome distribution was not altered. This suggests partial regulation of shoot development in the vegetative phase by SPL10. Meanwhile, the wide cauline leaves observed in the transgenic plants and the mutants were similar to those of fruitfull (ful) mutants. We found that FUL expression in leaves increased with shoot maturation and changed in SPL10 transgenic plants. FUL may function in shoot maturation under the control of SBP-box proteins.

MiR156-Regulated SPL Transcription Factors Define an Endogenous Flowering Pathway in Arabidopsis thaliana

The FT gene integrates several external and endogenous cues controlling flowering, including information on day length. A complex of the mobile FT protein and the bZIP transcription factor FD in turn has a central role in activating genes that execute the switch from vegetative to reproductive development. Here we reveal that microRNA156-targeted SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes not only act downstream of FT/FD, but also define a separate endogenous flowering pathway. High levels of miR156 in young plants prevent precocious flowering. A subsequent day length-independent decline in miR156 abundance provides a permissive environment for flowering and is paralleled by a rise in SPL levels. At the shoot apex, FT/FD and SPLs converge on an overlapping set of targets, with SPLs directly activating flower-promoting MADS box genes, providing a molecular substrate for both the redundant activities and the feed-forward action of the miR156/SPL and FT/FD modules in flowering control.

Function Annotation of an SBP-box Gene in Arabidopsis Based on Analysis of Co-expression Networks and Promoters

The SQUAMOSA PROMOTER BINDING PROTEIN–LIKE (SPL) gene family is an SBP-box transcription family in Arabidopsis. While several physiological responses to SPL genes have been reported, their biological role remains elusive. Here, we use a combined analysis of expression correlation, the interactome, and promoter content to infer the biological role of the SPL genes in Arabidopsis thaliana. Analysis of the SPL-correlated gene network reveals multiple functions for SPL genes. Network analysis shows that SPL genes function by controlling other transcription factor families and have relatives with membrane protein transport activity. The interactome analysis of the correlation genes suggests that SPL genes also take part in metabolism of glucose, inorganic salts, and ATP production. Furthermore, the promoters of the correlated genes contain a core binding cis-element (GTAC). All of these analyses suggest that SPL genes have varied functions in Arabidopsis.

Feminized tassels of maize mop1 and ts1 mutants exhibit altered levels of miR156 and specific SBP-box genes

Development of the unisexual maize inflorescences requires the abortion of pistillate primordia in the florets of the developing tassel and the arrest of staminate primordia in the florets of the developing ears. Mutations of many genes that lie within this sexual differentiation pathway, such as tasselseed1 (ts1), or that influence this pathway, such as mediator of paramutation 1 (mop1), result in feminization of the normally male tassel. Here, we show the loss of mop1 or ts1 function results in increased mRNA levels for several members of the SBP-box gene family. Our analyses of this family expand the number of maize SBP-box genes from 9 to 31 members. Intron-exon structures as well as phylogenetic data support the division of these family members into six groups. The SBP-box genes upregulated in feminized tassels fall into two groups, share common structural motifs and include the presence of a target site for miR156. Small RNA blots show miR156 levels are decreased in both mop1 and ts1 mutants. While there is a correlation between miR156 levels and SBP-box gene transcript levels, this correlation is not absolute, and thus we hypothesize that decreased levels of miR156 may provide competency for SBP-box gene upregulation by other common factors yet to be identified. We present a model that provides a putative link between ts1, ts2, ts4, Ts6, and mop1 in the sex-determination pathway.