scholarly journals A Nodule-Specific Gene Family from Alnus glutinosa Encodes Glycine- and Histidine-Rich Proteins Expressed in the Early Stages of Actinorhizal Nodule Development

1997 ◽  
Vol 10 (5) ◽  
pp. 656-664 ◽  
Author(s):  
Katharina Pawlowski ◽  
Paul Twigg ◽  
Svetlana Dobritsa ◽  
Changhui Guan ◽  
Beth C. Mullin
Keyword(s):  
Gene Family ◽  
Sequence Similarity ◽  
Root Nodules ◽  
Rna Stability ◽  
Alnus Glutinosa ◽  
Chelating Resin ◽  
Cdna Libraries ◽  
Nodule Development ◽  
Specific Gene ◽  
Signal Peptides

Two cDNAs representing different members (agNt84 and ag164) of a gene family encoding glycine- and histidinerich proteins have been isolated from cDNA libraries from Alnus glutinosa root nodules. Expression of the corresponding genes could only be detected in nodules. With in situ hybridization, the expression in nodules was found to occur in young, infected cells of the prefixation zone (zone 2). The encoded proteins contain putative signal peptides for targeting to the endomembrane system, sharing sequence similarity with signal peptides from plant glycinerich proteins, among them nodulin 24, a nodule-specific protein from soybean. This similarity suggests that, analogous to nodulin-24, proteins encoded by agNt84/ag164 may be located at the interface between the host plant membrane and the matrix surrounding the endosymbiont. The 3′untranslated regions of the cDNAs contain unusual poly(AT)n stretches that may play a role in the regulation of RNA stability. The protein encoded by agNt84 cDNA was expressed in Escherichia coli as a fusion with maltosebinding protein, and was shown to have the ability to bind to a nickel-chelating resin, indicating that it may function as a metal-binding protein.

scholarly journals Understanding the Early Evolutionary Stages of a Tandem Drosophilamelanogaster-Specific Gene Family: A Structural and Functional Population Study

2020 ◽  
Vol 37 (9) ◽  
pp. 2584-2600 ◽  
Author(s):  
Bryan D Clifton ◽  
Jamie Jimenez ◽  
Ashlyn Kimura ◽  
Zeinab Chahine ◽  
Pablo Librado ◽  
...  
Keyword(s):  
Gene Family ◽  
Sequence Similarity ◽  
Gene Families ◽  
Read Depth ◽  
Specific Gene ◽  
Protein Variant ◽  
Protein Coding ◽  
Expression Levels ◽  
Number Variation ◽  
Reference Quality

Abstract Gene families underlie genetic innovation and phenotypic diversification. However, our understanding of the early genomic and functional evolution of tandemly arranged gene families remains incomplete as paralog sequence similarity hinders their accurate characterization. The Drosophila melanogaster-specific gene family Sdic is tandemly repeated and impacts sperm competition. We scrutinized Sdic in 20 geographically diverse populations using reference-quality genome assemblies, read-depth methodologies, and qPCR, finding that ∼90% of the individuals harbor 3–7 copies as well as evidence of population differentiation. In strains with reliable gene annotations, copy number variation (CNV) and differential transposable element insertions distinguish one structurally distinct version of the Sdic region per strain. All 31 annotated copies featured protein-coding potential and, based on the protein variant encoded, were categorized into 13 paratypes differing in their 3′ ends, with 3–5 paratypes coexisting in any strain examined. Despite widespread gene conversion, the only copy present in all strains has functionally diverged at both coding and regulatory levels under positive selection. Contrary to artificial tandem duplications of the Sdic region that resulted in increased male expression, CNV in cosmopolitan strains did not correlate with expression levels, likely as a result of differential genome modifier composition. Duplicating the region did not enhance sperm competitiveness, suggesting a fitness cost at high expression levels or a plateau effect. Beyond facilitating a minimally optimal expression level, Sdic CNV acts as a catalyst of protein and regulatory diversity, showcasing a possible evolutionary path recently formed tandem multigene families can follow toward long-term consolidation in eukaryotic genomes.

scholarly journals Glycine-Rich Proteins Encoded by a Nodule-Specific Gene Family Are Implicated in Different Stages of Symbiotic Nodule Development in Medicago Spp.

2002 ◽  
Vol 15 (9) ◽  
pp. 922-931 ◽  
Author(s):  
Zoltán Kevei ◽  
José María Vinardell ◽  
György B. Kiss ◽  
Adam Kondorosi ◽  
Eva Kondorosi
Keyword(s):  
Bacterial Infection ◽  
Sinorhizobium Meliloti ◽  
Root Nodules ◽  
Gene Activation ◽  
Nodule Development ◽  
Specific Gene ◽  
Amino Terminal ◽  
Repeat Structure ◽  
Small Proteins ◽  
Genes Encoding

Four genes encoding small proteins with significantly high glycine content have been identified from root nodules of Medicago sativa. All of these proteins as well as their Medicago truncatula homologues carried an amino terminal signal peptide and a glycine-rich carboxy terminal domain. All except nodGRP3 lacked the characteristic repeat structure described for cell wall and stress response-related glycinerich proteins (GRP). Expression of these GRP genes was undetectable in flower, leaf, stem, and hypocotyl cells, whereas expression was highly induced during root nodule development, suggesting that GRP genes act as nodulins. Moreover, none of these nodule-expressed GRP genes were activated by hormones or stress treatments, which are inducers of many other GRPs. In Rhizobium-free spontaneous nodules and in nodules induced by a noninfective mutant strain of Sinorhizobium meliloti, all these genes were repressed, while they were induced in Fix¯ nodules, unaffected in bacterial infection, but halted in bacteroid differentiation. These results demonstrated that bacterial infection but not bacteroid differentiation is required for the induction of the nodule-specific GRP genes. Differences in kinetics and localization of gene activation as well as in the primary structure of proteins suggest nonredundant roles for these GRPs in nodule organogenesis.

ASSIMILATION OF NITROGEN IN ROOT NODULES OF ALDER (ALNUS GLUTINOSA)

1981 ◽  
Vol 89 (2) ◽  
pp. 321-326 ◽  
Author(s):  
JAN BLOM ◽  
WIM ROELOFSEN ◽  
ANTOON D. L. AKKERMANS
Keyword(s):  
Root Nodules ◽  
Alnus Glutinosa

scholarly journals Genome-wide analysis and expression profile of the bZIP gene family in poplar

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Kai Zhao ◽  
Song Chen ◽  
Wenjing Yao ◽  
Zihan Cheng ◽  
Boru Zhou ◽  
...  
Keyword(s):  
Salt Stress ◽  
Systems Biology ◽  
Gene Family ◽  
Stress Responses ◽  
Metal Ion ◽  
Gene Networks ◽  
Expression Patterns ◽  
Gene Set Enrichment Analysis ◽  
Specific Gene ◽  
Biological Processes

Abstract Background The bZIP gene family, which is widely present in plants, participates in varied biological processes including growth and development and stress responses. How do the genes regulate such biological processes? Systems biology is powerful for mechanistic understanding of gene functions. However, such studies have not yet been reported in poplar. Results In this study, we identified 86 poplar bZIP transcription factors and described their conserved domains. According to the results of phylogenetic tree, we divided these members into 12 groups with specific gene structures and motif compositions. The corresponding genes that harbor a large number of segmental duplication events are unevenly distributed on the 17 poplar chromosomes. In addition, we further examined collinearity between these genes and the related genes from six other species. Evidence from transcriptomic data indicated that the bZIP genes in poplar displayed different expression patterns in roots, stems, and leaves. Furthermore, we identified 45 bZIP genes that respond to salt stress in the three tissues. We performed co-expression analysis on the representative genes, followed by gene set enrichment analysis. The results demonstrated that tissue differentially expressed genes, especially the co-expressing genes, are mainly involved in secondary metabolic and secondary metabolite biosynthetic processes. However, salt stress responsive genes and their co-expressing genes mainly participate in the regulation of metal ion transport, and methionine biosynthetic. Conclusions Using comparative genomics and systems biology approaches, we, for the first time, systematically explore the structures and functions of the bZIP gene family in poplar. It appears that the bZIP gene family plays significant roles in regulation of poplar development and growth and salt stress responses through differential gene networks or biological processes. These findings provide the foundation for genetic breeding by engineering target regulators and corresponding gene networks into poplar lines.

Meiotic Recombination Between Paralogous RBCSB Genes on Sister Chromatids of Arabidopsis thaliana

Genetics ◽  
2004 ◽  
Vol 166 (2) ◽  
pp. 947-957 ◽  
Author(s):  
John G Jelesko ◽  
Kristy Carter ◽  
Whitney Thompson ◽  
Yuki Kinoshita ◽  
Wilhelm Gruissem
Keyword(s):  
Gene Cluster ◽  
Dna Sequences ◽  
Meiotic Recombination ◽  
Sequence Similarity ◽  
Specific Gene ◽  
High Sequence Similarity ◽  
Paralogous Genes ◽  
Chimeric Genes ◽  
Unequal Recombination ◽  
Sister Chromatids

Abstract Paralogous genes organized as a gene cluster can rapidly evolve by recombination between misaligned paralogs during meiosis, leading to duplications, deletions, and novel chimeric genes. To model unequal recombination within a specific gene cluster, we utilized a synthetic RBCSB gene cluster to isolate recombinant chimeric genes resulting from meiotic recombination between paralogous genes on sister chromatids. Several F1 populations hemizygous for the synthRBCSB1 gene cluster gave rise to Luc+ F2 plants at frequencies ranging from 1 to 3 × 10-6. A nonuniform distribution of recombination resolution sites resulted in the biased formation of recombinant RBCS3B/1B::LUC genes with nonchimeric exons. The positioning of approximately half of the mapped resolution sites was effectively modeled by the fractional length of identical DNA sequences. In contrast, the other mapped resolution sites fit an alternative model in which recombination resolution was stimulated by an abrupt transition from a region of relatively high sequence similarity to a region of low sequence similarity. Thus, unequal recombination between paralogous RBCSB genes on sister chromatids created an allelic series of novel chimeric genes that effectively resulted in the diversification rather than the homogenization of the synthRBCSB1 gene cluster.

Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements

2021 ◽  
pp. gr.275658.121
Author(s):  
Yuyun Zhang ◽  
Zijuan Li ◽  
Yu'e Zhang ◽  
Kande Lin ◽  
Yuan Peng ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Genome Evolution ◽  
Regulatory Networks ◽  
Transcriptional Regulatory Network ◽  
Sequence Similarity ◽  
Purifying Selection ◽  
Wheat Genome ◽  
Specific Gene ◽  
High Sequence Similarity ◽  
Wheat Genome Evolution

More than 80% of the wheat genome consists of transposable elements (TEs), which act as one major driver of wheat genome evolution. However, their contributions to the regulatory evolution of wheat adaptations remain largely unclear. Here, we created genome-binding maps for 53 transcription factors (TFs) underlying environmental responses by leveraging DAP-seq in Triticum urartu, together with epigenomic profiles. Most TF-binding sites (TFBS) located distally from genes are embedded in TEs, whose functional relevance is supported by purifying selection and active epigenomic features. About 24% of the non-TE TFBS share significantly high sequence similarity with TE-embedded TFBS. These non-TE TFBS have almost no homologous sequences in non-Triticeae species and are potentially derived from Triticeae-specific TEs. The expansion of TE-derived TFBS linked to wheat-specific gene responses, suggesting TEs are an important driving force for regulatory innovations. Altogether, TEs have been significantly and continuously shaping regulatory networks related to wheat genome evolution and adaptation.

pha-4 is Ce-fkh-1, a fork head/HNF-3alpha, beta, gamma homolog that functions in organogenesis of the C. elegans pharynx

Development ◽  
1998 ◽  
Vol 125 (12) ◽  
pp. 2171-2180 ◽  
Author(s):  
J.M. Kalb ◽  
K.K. Lau ◽  
B. Goszczynski ◽  
T. Fukushige ◽  
D. Moons ◽  
...  
Keyword(s):  
Early Stage ◽  
Sequence Similarity ◽  
Expression Patterns ◽  
Ectopic Expression ◽  
Specific Gene ◽  
Gata Factor ◽  
Enhancer Element ◽  
C Elegans ◽  
Fork Head ◽  
Organ Identity

The C. elegans Ce-fkh-1 gene has been cloned on the basis of its sequence similarity to the winged-helix DNA binding domain of the Drosophila fork head and mammalian HNF-3alpha, beta, gamma genes, and mutations in the zygotically active pha-4 gene have been shown to block formation of the pharynx (and rectum) at an early stage in embryogenesis. In the present paper, we show that Ce-fkh-1 and pha-4 are the same gene. We show that PHA-4 protein is present in nuclei of essentially all pharyngeal cells, of all five cell types. PHA-4 protein first appears close to the point at which a cell lineage will produce only pharyngeal cells, independently of cell type. We show that PHA-4 binds directly to a ‘pan-pharyngeal enhancer element’ previously identified in the promoter of the pharyngeal myosin myo-2 gene; in transgenic embryos, ectopic PHA-4 activates ectopic myo-2 expression. We also show that ectopic PHA-4 can activate ectopic expression of the ceh-22 gene, a pharyngeal-specific NK-2-type homeodomain protein previously shown to bind a muscle-specific enhancer near the PHA-4 binding site in the myo-2 promoter. We propose that it is the combination of pha-4 and regulatory molecules such as ceh-22 that produces the specific gene expression patterns during pharynx development. Overall, pha-4 can be described as an ‘organ identity factor’, completely necessary for organ formation, present in all cells of the organ from the earliest stages, capable of integrating upstream developmental pathways (in this case, the two distinct pathways that produce the anterior and posterior pharynx) and participating directly in the transcriptional regulation of organ specific genes. Finally, we note that the distribution of PHA-4 protein in C. elegans embryos is remarkably similar to the distribution of the fork head protein in Drosophila embryos: high levels in the foregut/pharynx and hindgut/rectum; low levels in the gut proper. Moreover, we show that pha-4 expression in the C. elegans gut is regulated by elt-2, a C. elegans gut-specific GATA-factor and possible homolog of the Drosophila gene serpent, which influences fork head expression in the fly gut. Overall, our results provide evidence for a highly conserved pathway regulating formation of the digestive tract in all (triploblastic) metazoa.

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