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PubMed2000

Mining of assembled expressed sequence tag (EST) data for protein families: application to the G protein-coupled receptor superfamily.

The availability of large expressed sequence tag (EST) databases has led to a revolution in the way new genes are identified. Mining of these databases using known protein sequences as queries is a powerful technique for discovering orthologous and paralogous genes. The scientist is often confronted, however, by an enormous amount of search output owing to the inherent redundancy of EST data. In addition, high search sensitivity often cannot be achieved using only a single member of a protein superfamily as a query. In this paper a technique for addressing both of these issues is described. Assembled EST databases are queried with every member of a protein superfamily, the results are integrated and false positives are pruned from the set. The result is a set of assemblies enriched in members of the protein superfamily under consideration. The technique is applied to the G protein-coupled receptor (GPCR) superfamily in the construction of a GPCR Resource. A novel full-length human GPCR identified from the GPCR Resource is presented, illustrating the utility of the method.

Amino Acid Sequence↗

PubMed2000

The TIGR gene indices: reconstruction and representation of expressed gene sequences.

Expressed sequence tags (ESTs) have provided a first glimpse of the collection of transcribed sequences in a variety of organisms. However, a careful analysis of this sequence data can provide significant additional functional, structural and evolutionary information. Our analysis of the public EST sequences, available through the TIGR Gene Indices (TGI; http://www.tigr.org/tdb/tdb.html ), is an attempt to identify the genes represented by that data and to provide additional information regarding those genes. Gene Indices are constructed for selected organisms by first clustering, then assembling EST and annotated gene sequences from GenBank. This process produces a set of unique, high-fidelity virtual transcripts, or tentative consensus (TC) sequences. The TC sequences can be used to provide putative genes with functional annotation, to link the transcripts to mapping and genomic sequence data, and to provide links between orthologous and paralogous genes.

Base Sequence↗

PubMed2004

Preferential binding to branched DNA strands and strand-annealing activity of the human Rad51B, Rad51C, Rad51D and Xrcc2 protein complex.

The Rad51B, Rad51C, Rad51D and Xrcc2 proteins are Rad51 paralogs, and form a complex (BCDX2 complex) in mammalian cells. Mutant cells defective in any one of the Rad51-paralog genes exhibit spontaneous genomic instability and extreme sensitivity to DNA-damaging agents, due to inefficient recombinational repair. Therefore, the Rad51 paralogs play important roles in the maintenance of genomic integrity through recombinational repair. In the present study, we examined the DNA-binding preference of the human BCDX2 complex. Competitive DNA-binding assays using seven types of DNA substrates, single-stranded DNA (ssDNA), double-stranded DNA, 5'- and 3'-tailed duplexes, nicked duplex DNA, Y-shaped DNA and a synthetic Holliday junction, revealed that the BCDX2 complex preferentially bound to the two DNA substrates with branched structures (the Y-shaped DNA and the synthetic Holliday junction). Furthermore, the BCDX2 complex catalyzed the strand-annealing reaction between a long linear ssDNA (1.2 kb in length) and its complementary circular ssDNA. These properties of the BCDX2 complex may be important for its roles in the maintenance of chromosomal integrity.

Adenosine Triphosphatases↗

PubMed2005

LIM-homeodomain genes as territory markers in the brainstem of adult and developing Xenopus laevis.

We investigated expression patterns of the LIM-homeodomain (LIM-hd) genes x-Lhx1, x-Lhx2, x-Lhx5, and x-Lhx9 in the brainstem of Xenopus laevis during larval development and in the adult. The two groups of paralogous genes, x-Lhx1/x-Lhx5 and x-Lhx2/x-Lhx9, showed fundamentally different expression patterns, being expressed in ventral versus dorsal territories of the midbrain and hindbrain, respectively. Indeed, prominent expression of x-Lhx1/5 was found in the mesencephalic tegmentum and the hindbrain reticular formation, whereas conspicuous x-Lhx2/9 expression was observed in the torus semicircularis and isthmic nucleus. A few shared expression domains for the two pairs of paralogs included the optic tectum and the anterodorsal and pedunculopontine nuclei. In each structure, expression of the two paralogs was almost identical, indicating that the regulation of their expression in this part of the brain has evolved slightly since gene duplication occurred. Notable exceptions included the expression of x-Lhx1 but not x-Lhx5 in the Purkinje cells and the expression of x-Lhx9 but not x-Lhx2 in the lateral line nucleus. The analysis of LIM-hd expression patterns throughout development allowed the origin of given structures in early embryos to be traced back. x-Lhx1 and x-Lhx5 were relevant to locate the cerebellar anlage and to follow morphogenesis of the cerebellar plate and cerebellar nuclei. They also highlighted the rhombomeric organization of the hindbrain. On the other hand, x-Lhx2 and x-Lhx9 showed a dynamic spatiotemporal pattern relative to tectal development and layering, and x-Lhx9 was useful to trace back the origin of the isthmus in early development.

Animals↗

PubMed2004

Computational inference of scenarios for alpha-proteobacterial genome evolution.

The alpha-proteobacteria, from which mitochondria are thought to have originated, display a 10-fold genome size variation and provide an excellent model system for studies of genome size evolution in bacteria. Here, we use computational approaches to infer ancestral gene sets and to quantify the flux of genes along the branches of the alpha-proteobacterial species tree. Our study reveals massive gene expansions at branches diversifying plant-associated bacteria and extreme losses at branches separating intracellular bacteria of animals and humans. Alterations in gene numbers have mostly affected functional categories associated with regulation, transport, and small-molecule metabolism, many of which are encoded by paralogous gene families located on auxiliary chromosomes. The results suggest that the alpha-proteobacterial ancestor contained 3,000-5,000 genes and was a free-living, aerobic, and motile bacterium with pili and surface proteins for host cell and environmental interactions. Approximately one third of the ancestral gene set has no homologs among the eukaryotes. More than 40% of the genes without eukaryotic counterparts encode proteins that are conserved among the alpha-proteobacteria but for which no function has yet been identified. These genes that never made it into the eukaryotes but are widely distributed in bacteria may represent bacterial drug targets and should be prime candidates for future functional characterization.

Alphaproteobacteria↗

PubMed2007

Conservation, convergence, and divergence of light-responsive, circadian-regulated, and tissue-specific expression patterns during evolution of the Arabidopsis GATA gene family.

In vitro analyses of plant GATA transcription factors have implicated some proteins in light-mediated and circadian-regulated gene expression, and, more recently, the analysis of mutants has uncovered further diverse roles for plant GATA factors. To facilitate function discovery for the 29 GATA genes in Arabidopsis (Arabidopsis thaliana), we have experimentally verified gene structures and determined expression patterns of all family members across adult tissues and suspension cell cultures, as well as in response to light and signals from the circadian clock. These analyses have identified two genes that are strongly developmentally light regulated, expressed predominantly in photosynthetic tissue, and with transcript abundance peaking before dawn. In contrast, several GATA factor genes are light down-regulated. The products of these light-regulated genes are candidates for those proteins previously implicated in light-regulated transcription. Coexpression of these genes with well-characterized light-responsive transcripts across a large microarray data set supports these predictions. Other genes show additional tissue-specific expression patterns suggesting novel and unpredicted roles. Genome-wide analysis using coexpression scatter plots for paralogous gene pairs reveals unexpected differences in cocorrelated gene expression profiles. Clustering the Arabidopsis GATA factor gene family by similarity of expression patterns reveals that genes of recent descent do not uniformly show conserved current expression profiles, yet some genes showing more distant evolutionary origins have acquired common expression patterns. In addition to defining developmental and environmental dynamics of GATA transcript abundance, these analyses offer new insights into the evolution of gene expression profiles following gene duplication events.

Amino Acid Motifs↗

PubMed1983

Genetics and evolution of multilocus isozymes in hexaploid wheat.

Aneuploid genetic studies of isozyme variation in cv Chinese Spring have disclosed that numerous enzymes of hexaploid wheat exist in multiple molecular forms as a direct consequence of polyploidy. Sixty-nine isozyme structural genes have been identified to date. Two of these belong to a duplicate set and at least 54 to triplicate sets of paralogous genes that are located one each in related chromosomes in different genomes. Each of these gene sets encodes either two or three isozymes. The role of regional gene duplication in the production of multilocus isozymes in hexaploid wheat is as yet poorly understood, although a considerable amount of indirect evidence suggests that a large number of isozymes are encoded by genes that were produced by ancient regional gene duplication events in a genome ancestral to the genomes now present in the species. A full assessment of the role of regional gene duplication in the production of hexaploid wheat isozymes must await further studies. The isozyme structural gene locations thus far determined indicate that the gene synteny relationships that existed in the ancestral wheat genome are in large part conserved in each of the three genomes of cv Chinese Spring and that the genetic content of most individual chromosome arms has also been in large part conserved.

Biological Evolution↗

PubMed2005

Divide-and-conquer approach for the exemplar breakpoint distance.

MOTIVATION: A one-to-one correspondence between the sets of genes in the two genomes being compared is necessary for the notions of breakpoint and reversal distances. To compare genomes where there are paralogous genes, Sankoff formulated the exemplar distance problem as a general version of the genome rearrangement problem. Unfortunately, the problem is NP-hard even for the breakpoint distance. RESULTS: This paper proposes a divide-and-conquer approach for calculating the exemplar breakpoint distance between two genomes with multiple gene families. The combination of our approach and Sankoff's branch-and-bound technique leads to a practical program to answer this question. Tests with both simulated and real datasets show that our program is much more efficient than the existing program that is based only on the branch-and-bound technique. AVAILABILITY: Code for the program is available from the authors.

Algorithms↗

PubMed2003

What's in the genome of a filamentous fungus? Analysis of the Neurospora genome sequence.

The German Neurospora Genome Project has assembled sequences from ordered cosmid and BAC clones of linkage groups II and V of the genome of Neurospora crassa in 13 and 12 contigs, respectively. Including additional sequences located on other linkage groups a total of 12 Mb were subjected to a manual gene extraction and annotation process. The genome comprises a small number of repetitive elements, a low degree of segmental duplications and very few paralogous genes. The analysis of the 3218 identified open reading frames provides a first overview of the protein equipment of a filamentous fungus. Significantly, N.crassa possesses a large variety of metabolic enzymes including a substantial number of enzymes involved in the degradation of complex substrates as well as secondary metabolism. While several of these enzymes are specific for filamentous fungi many are shared exclusively with prokaryotes.

Chromosome Mapping↗

PubMed1999

OsMADS13, a novel rice MADS-box gene expressed during ovule development.

MADS-box genes have been shown to play a major role in defining plant architecture. Recently, several MADS-box genes have been reported that are highly expressed in the ovule. However, only for the Petunia genes FBP7 and FBP11 has a function in defining ovule identity been shown. We have isolated a rice MADS-box gene named OsMADS13. Expression analysis has shown that this gene is highly expressed in developing ovules. In order to facilitate a detailed characterization of rice ovule-expressed genes, a comprehensive morphological description of ovule development in rice has been performed. The predicted amino acid sequence of OsMADS13 shows significant homology with ZAG2, a maize MADS-box gene, which is also expressed mainly in the ovule. Mapping of the gene in the rice genome showed that it is located on chromosome 12, which is syntenic to two maize regions where ZAG2 and its paralogous gene ZMM1 have been mapped. Our results suggest that OsMADS13 is the ortholog of ZAG2 and ZMM1 and might play a role in rice ovule and seed development.

Amino Acid Sequence↗

PubMed1992

HOX gene expression in normal and neoplastic human kidney.

As a consequence of transformation, cancer cells generally lose some of their differentiative properties. Thus, alterations interfering with the genetic mechanisms required to maintain embryonic determination could lead to tumorigenesis. Homeobox genes are a network of genes encoding nuclear proteins containing DNA-binding homeodomains that are highly conserved throughout evolution. They are expressed in a stage-related fashion in the developing embryo and, in adult life, in normal tissues. In mice and humans, homeobox genes of the HOX family are organized in 4 clusters on different chromosomes which have presumably evolved by duplication of a primordial gene cluster. Strikingly, the order of genes within each cluster is also highly conserved throughout evolution, suggesting that the physical organization of HOX genes might be essential for their expression. Recent reports indicate that homeobox mutant mice display morphological abnormalities or show neoplastic alterations, and that growth factors can turn on homeobox genes. We have studied the expression of the Antennapedia-like HOX genes in normal human kidney and in renal carcinomas. The great majority of the HOX genes analyzed are expressed in a peculiar manner in normal kidney: blocks of genes, even entire HOX loci, are coordinately regulated. Alterations in HOX gene expression in renal carcinoma can be observed in 2 genes of the HOX-2 locus, HOX-2A and HOX-2E, which are actively expressed in normal kidney and silent in cancer biopsies. The HOX-3H gene is not expressed in normal kidney whereas the HOX-3H transcripts are present in renal carcinomas. Homeobox genes within the 4 HOX loci can be aligned on the basis of the maximal sequence homology of their homeodomains: this alignment defines 13 paralogous gene groups. In renal carcinomas, genes of group 10 (HOX-1D, 2F, 3E, 4B) display a marked difference in their transcript classes when compared to those of normal kidney. Our findings suggest an association between altered HOX gene expression and kidney cancer.

Carcinoma, Renal Cell↗

PubMed2005

Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability.

Pseudogenes, in the case of protein-coding genes, are gene copies that have lost the ability to code for a protein; they are typically identified through annotation of disabled, decayed or incomplete protein-coding sequences. Processed pseudogenes (PPsigs) are made through mRNA retrotransposition. There is overwhelming genomic evidence for thousands of human PPsigs and also dozens of human processed genes that comprise complete retrotransposed copies of other genes. Here, we survey for an intermediate entity, the transcribed processed pseudogene (TPPsig), which is disabled but nonetheless transcribed. TPPsigs may affect expression of paralogous genes, as observed in the case of the mouse makorin1-p1 TPPsig. To elucidate their role, we identified human TPPsigs by mapping expressed sequences onto PPsigs and, reciprocally, extracting TPPsigs from known mRNAs. We consider only those PPsigs that are homologous to either non-mammalian eukaryotic proteins or protein domains of known structure, and require detection of identical coding-sequence disablements in both the expressed and genomic sequences. Oligonucleotide microarray data provide further expression verification. Overall, we find 166-233 TPPsigs ( approximately 4-6% of PPsigs). Proteins/transcripts with the highest numbers of homologous TPPsigs generally have many homologous PPsigs and are abundantly expressed. TPPsigs are significantly over-represented near both the 5' and 3' ends of genes; this suggests that TPPsigs can be formed through gene-promoter co-option, or intrusion into untranslated regions. However, roughly half of the TPPsigs are located away from genes in the intergenic DNA and thus may be co-opting cryptic promoters of undesignated origin. Furthermore, TPPsigs are unlike other PPsigs and processed genes in the following ways: (i) they do not show a significant tendency to either deposit on or originate from the X chromosome; (ii) only 5% of human TPPsigs have potential orthologs in mouse. This latter finding indicates that the vast majority of TPPsigs is lineage specific. This is likely linked to well-documented extensive lineage-specific SINE/LINE activity. The list of TPPsigs is available at: http://www.biology.mcgill.ca/faculty/harrison/tppg/bppg.tov (or) http:pseudogene.org.

Amino Acid Sequence↗

PubMed1997

Protein evolution viewed through Escherichia coli protein sequences: introducing the notion of a structural segment of homology, the module.

Paralogous genes are genes which descend from a progenitor gene which has duplicated as an ancestral gene, each copy having diverged prior to speciation. With comprehensive information available on functions of Escherichia coli proteins, analysis of sequence-related E. coli paralogous proteins can give information on the early ancestors of families of proteins now residing in many contemporary organisms, such as the enzymes of metabolism, some kinds of transport mechanisms and some kinds of regulatory mechanisms. In the first step, we have confirmed that E. coli contains a very high proportion of paralogous proteins. Next, we have defined two main classes of paralogous proteins. One class is formed of proteins which contain a unique structural segment homologous to a single set of related proteins. The other class corresponds to proteins which contain more than one structural segment of homology, each segment homologous to unrelated sets of proteins. We define such an independent structural segment of homology as a module. This modular structure (mean length equivalent to 209 amino acids) corresponds often to entire proteins, but there are also proteins that appear to be assembled from two or three independent modules having independent origins. Most multimodular proteins appear to have been formed early in their history, a minority appear to be relatively recent fusions of independent modules. Examining 1404 independent structural segments of homology, composed of both modules and entire proteins, we found that the segments of homology fell into 352 sequence-related groups or families. The majority of these families (ranging from 2 to 62 members) are functionally homogeneous. This strongly suggests that the 1404 present-day modules and proteins derive from a minimal set of 352 ancestral modules, each one being already of the same size and having a function similar to all members of its progeny.

Bacterial Proteins↗

PubMed2005

Genome-wide comparative analysis of the IQD gene families in Arabidopsis thaliana and Oryza sativa.

BACKGROUND: Calcium signaling plays a prominent role in plants for coordinating a wide range of developmental processes and responses to environmental cues. Stimulus-specific generation of intracellular calcium transients, decoding of calcium signatures, and transformation of the signal into cellular responses are integral modules of the transduction process. Several hundred proteins with functions in calcium signaling circuits have been identified, and the number of downstream targets of calcium sensors is expected to increase. We previously identified a novel, calmodulin-binding nuclear protein, IQD1, which stimulates glucosinolate accumulation and plant defense in Arabidopsis thaliana. Here, we present a comparative genome-wide analysis of a new class of putative calmodulin target proteins in Arabidopsis and rice. RESULTS: We identified and analyzed 33 and 29 IQD1-like genes in Arabidopsis thaliana and Oryza sativa, respectively. The encoded IQD proteins contain a plant-specific domain of 67 conserved amino acid residues, referred to as the IQ67 domain, which is characterized by a unique and repetitive arrangement of three different calmodulin recruitment motifs, known as the IQ, 1-5-10, and 1-8-14 motifs. We demonstrated calmodulin binding for IQD20, the smallest IQD protein in Arabidopsis, which consists of a C-terminal IQ67 domain and a short N-terminal extension. A striking feature of IQD proteins is the high isoelectric point (approximately 10.3) and frequency of serine residues (approximately 11%). We compared the Arabidopsis and rice IQD gene families in terms of gene structure, chromosome location, predicted protein properties and motifs, phylogenetic relationships, and evolutionary history. The existence of an IQD-like gene in bryophytes suggests that IQD proteins are an ancient family of calmodulin-binding proteins and arose during the early evolution of land plants. CONCLUSION: Comparative phylogenetic analyses indicate that the major IQD gene lineages originated before the monocot-eudicot divergence. The extant IQD loci in Arabidopsis primarily resulted from segmental duplication and reflect preferential retention of paralogous genes, which is characteristic for proteins with regulatory functions. Interaction of IQD1 and IQD20 with calmodulin and the presence of predicted calmodulin binding sites in all IQD family members suggest that IQD proteins are a new class of calmodulin targets. The basic isoelectric point of IQD proteins and their frequently predicted nuclear localization suggest that IQD proteins link calcium signaling pathways to the regulation of gene expression. Our comparative genomics analysis of IQD genes and encoded proteins in two model plant species provides the first step towards the functional dissection of this emerging family of putative calmodulin targets.

Arabidopsis↗

PubMed2005

Phylogenomic analysis and expression patterns of large Maf genes in Xenopus tropicalis provide new insights into the functional evolution of the gene family in osteichthyans.

We have performed an exhaustive characterization of the large Maf family of basic leucine zipper transcription factors in vertebrates using the genome data available, and studied the embryonic expression patterns of the four paralogous genes thus identified in Xenopus tropicalis. Our phylogenetic analysis shows that, in osteichthyans, the large Maf family contains four orthology classes, MafA, MafB, c-Maf and Nrl, which have emerged in vertebrates prior to the split between actinopterygians and sarcopterygians. It leads to the unambiguous assignment of the Xenopus laevis XLmaf gene, previously considered a MafA orthologue, to the Nrl class, the identification of the amphibian MafA and c-Maf orthologues and the identification of the zebrafish Nrl gene. The four X. tropicalis paralogues display partially redundant but nevertheless distinct expression patterns in the somites, developing hindbrain, pronephros, ventral blood island and lens. Comparisons with the data available in the mouse, chick and zebrafish show that these large Maf expression territories are highly conserved among osteichthyans but also highlight a number of differences in the timing of large Maf gene expression, the precise extent of some labelled territories and the combinations of paralogues transcribed in some organs. In particular, the availability of robust phylogenies leads to a reinterpretation of previous expression pattern comparisons, suggesting an important part for function shuffling within the gene family in the developing lens. These data highlight the importance of exhaustive characterizations of gene families for comparative analyses of the genetic mechanisms, which control developmental processes in vertebrates.

Animals↗

PubMed1999

Comparison of Bombyx mori and Helicoverpa armigera cytoplasmic actin genes provides clues to the evolution of actin genes in insects.

The cytoplasmic actin genes BmA3 and BmA4 of Bombyx mori were found clustered in a single genomic clone in the same orientation. As a similar clustering of the two cytoplasmic actin genes Ha3a and Ha3b also occurs in another lepidopteran, Helicoverpa armigera, we analyzed the sequence of the pair of genes from each species. Due to the high conservation of cytoplasmic actins, the coding sequence of the four genes was easily aligned, allowing the detection of similarities in noncoding exon and intron sequences as well as in flanking sequences. All four genes exhibited a conserved intron inserted in codon 117, an original position not encountered in other species. It can thus be postulated that all of these genes derived from a common ancestral gene carrying this intron after a single event of insertion. The comparison of the four genes revealed that the genes of B. mori and H. armigera are related in two different ways: the coding sequence and the intron that interrupts it are more similar between paralogous genes within each species than between orthologous genes of the two species. In contrast, the other (noncoding) regions exhibited the greatest similarity between a gene of one species and a gene of the other species, defining two pairs of orthologous genes, BmA3 and HaA3a on one hand and BmA4 and HaA3b on the other. However, in each species, the very high similarities of the coding sequence and of the single intron that interrupts it strongly suggest that gene conversion events have homogenized this part of the sequence. As the divergence of the B. mori genes was higher than that of the H. armigera genes, we postulated that the gene conversion occurred earlier in the B. mori lineage. This leads us to hypothesize that gene conversion could also be responsible for the original transfer of the common intron to the second gene copy before the divergence of the B. mori and H. armigera lineages.

3' Untranslated Regions↗

PubMed2005

The ClgR protein regulates transcription of the clpP operon in Bifidobacterium breve UCC 2003.

Five clp genes (clpC, clpB, clpP1, clpP2, and clpX), representing chaperone- and protease-encoding genes, were previously identified in Bifidobacterium breve UCC 2003. In the present study, we characterize the B. breve UCC 2003 clpP locus, which consists of two paralogous genes, designated clpP1 and clpP2, whose deduced protein products display significant similarity to characterized ClpP peptidases. Transcriptional analyses showed that the clpP1 and clpP2 genes are transcribed in response to moderate heat shock as a bicistronic unit with a single promoter. The role of a clgR homologue, known to control the regulation of clpP gene expression in Streptomyces lividans and Corynebacterium glutamicum, was investigated by gel mobility shift assays and DNase I footprint experiments. We show that ClgR, which in its purified form appears to exist as a dimer, requires a proteinaceous cofactor to assist in specific binding to a 30-bp region of the clpP promoter region. In pull-down experiments, a 56-kDa protein copurified with ClgR, providing evidence that the two proteins also interact in vivo and that the copurified protein represents the cofactor required for ClgR activity. The prediction of the ClgR three-dimensional structure provides further insights into the binding mode of this protein to the clpP1 promoter region and highlights the key amino acid residues believed to be involved in the protein-DNA interaction.

Adaptation, Physiological↗

PubMed2005

Members of TALE and WUS subfamilies of homeodomain proteins with potentially important functions in development form dimers within each subfamily in rice.

Transacting factors often form homo- and heterodimers and regulate various targets, the type of regulation depending on the dimeric combination. The WUS and TALE subfamilies are two atypical homeodomains in plants. A homeodomain mediates sequence-specific binding to its target DNA and usually consists of 60 amino acid residues, whereas atypical homeodomains have extra amino acid residues in the well-conserved region. The genes OsWUS and OsPRS, which encode atypical homeodomain proteins from the WUS subfamily, and OsBEL and OSH15, which encode those from the TALE subfamily, were isolated from rice and tested for their interactions by yeast two-hybrid analysis. OsWUS and OsPRS formed homodimers and formed heterodimers with each other but did not form dimers with the TALE family homeodomain proteins OSH15 or OsBEL. Likewise, OSH15 and OsBEL formed homodimers and heterodimers but did not form dimers with the WUS family homeodomain proteins OsWUS and OsPRS. These findings suggest that the combinations of dimers are well correlated with the classification of these proteins on the basis of sequence similarity. RT-PCR analysis revealed that expression of OsWUS and OsPRS was detected in the same organs, namely floral buds, roots, and suspension cells. Therefore, it is possible that the proteins encoded by both of these genes function as homo- and heterodimers in planta. These results suggest that, during the evolution of these subfamilies, various combinations of dimers within proteins encoded by paralogous genes were formed and generated independent regulatory networks that enabled complex patterns of plant development.

Base Sequence↗