Browsing by Subject "genome"

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Adaptive Expansion of the Maize Maternally Expressed Gene (Meg) Family involves Changes in Expression Patterns and Protein Secondary Structures of its Members
(2014-08) Xiong, Yuqing; Mei, Wenbin; Kim, Eun-Deok; Mukherjee, Krishanu; Hassanein, Hatem; Barbazuk, William Brad; Sung, Sibum; Kolaczkowski, Bryan; Kang, Byung-Ho; Kim, Eun-Deok; Sung, Sibum
The Maternally expressed gene (Meg) family is a locally-duplicated gene family of maize which encodes cysteine-rich proteins (CRPs). The founding member of the family, Meg1, is required for normal development of the basal endosperm transfer cell layer (BETL) and is involved in the allocation of maternal nutrients to growing seeds. Despite the important roles of Meg1 in maize seed development, the evolutionary history of the Meg cluster and the activities of the duplicate genes are not understood. Results: In maize, the Meg gene cluster resides in a 2.3 Mb-long genomic region that exhibits many features of non-centromeric heterochromatin. Using phylogenetic reconstruction and syntenic alignments, we identified the pedigree of the Meg family, in which 11 of its 13 members arose in maize after allotetraploidization similar to 4.8 mya. Phylogenetic and population-genetic analyses identified possible signatures suggesting recent positive selection in Meg homologs. Structural analyses of the Meg proteins indicated potentially adaptive changes in secondary structure from alpha-helix to beta-strand during the expansion. Transcriptomic analysis of the maize endosperm indicated that 6 Meg genes are selectively activated in the BETL, and younger Meg genes are more active than older ones. In endosperms from B73 by Mo17 reciprocal crosses, most Meg genes did not display parent-specific expression patterns. Conclusions: Recently-duplicated Meg genes have different protein secondary structures, and their expressions in the BETL dominate over those of older members. Together with the signs of positive selections in the young Meg genes, these results suggest that the expansion of the Meg family involves potentially adaptive transitions in which new members with novel functions prevailed over older members.
Buffering by Gene Duplicates: An Analysis of Molecular Correlates and Evolutionary Conservation
(2008-12) Hannay, Kevin; Marcotte, Edward M.; Vogel, Christine; Hannay, Kevin; Marcotte, Edward M.; Vogel, Christine
One mechanism to account for robustness against gene knockouts or knockdowns is through buffering by gene duplicates, but the extent and general correlates of this process in organisms is still a matter of debate. To reveal general trends of this process, we provide a comprehensive comparison of gene essentiality, duplication and buffering by duplicates across seven bacteria (Mycoplasma genitalium, Bacillus subtilis, Helicobacter pylori, Haemophilus influenzae, Mycobacterium tuberculosis, Pseudomonas aeruginosa, Escherichia coli), and four eukaryotes (Saccharomyces cerevisiae (yeast), Caenorhabditis elegans (worm), Drosophila melanogaster (fly), Mus musculus (mouse)). Results: In nine of the eleven organisms, duplicates significantly increase chances of survival upon gene deletion (P-value <= 0.05), but only by up to 13%. Given that duplicates make up to 80% of eukaryotic genomes, the small contribution is surprising and points to dominant roles of other buffering processes, such as alternative metabolic pathways. The buffering capacity of duplicates appears to be independent of the degree of gene essentiality and tends to be higher for genes with high expression levels. For example, buffering capacity increases to 23% amongst highly expressed genes in E. coli. Sequence similarity and the number of duplicates per gene are weak predictors of the duplicate's buffering capacity. In a case study we show that buffering gene duplicates in yeast and worm are somewhat more similar in their functions than non-buffering duplicates and have increased transcriptional and translational activity. Conclusion: In sum, the extent of gene essentiality and buffering by duplicates is not conserved across organisms and does not correlate with the organisms' apparent complexity. This heterogeneity goes beyond what would be expected from differences in experimental approaches alone. Buffering by duplicates contributes to robustness in several organisms, but to a small extent - and the relatively large amount of buffering by duplicates observed in yeast and worm may be largely specific to these organisms. Thus, the only common factor of buffering by duplicates between different organisms may be the by-product of duplicate retention due to demands of high dosage.
Complete Plastome Sequence of Thalictrum Coreanum (Ranunculaceae) and Transfer of the rpl32 Gene to the Nucleus in the Ancestor of the Subfamily Thalictroideae
(2015-02) Park, Seongjun; Jansen, Robert K.; Park, SeonJoo; Park, Seongjun; Jansen, Robert K.; Park, SeonJoo
Plastids originated from cyanobacteria and the majority of the ancestral genes were lost or functionally transferred to the nucleus after endosymbiosis. Comparative genomic investigations have shown that gene transfer from plastids to the nucleus is an ongoing evolutionary process but molecular evidence for recent functional gene transfers among seed plants have only been documented for the four genes accD, infA, rpl22, and rpl32. Results: The complete plastid genome of Thalictrum coreanum, the first from the subfamily Thalictroideae (Ranunculaceae), was sequenced and revealed the losses of two genes, infA and rpl32. The functional transfer of these two genes to the nucleus in Thalictrum was verified by examination of nuclear transcriptomes. A survey of the phylogenetic distribution of the rpl32 loss was performed using 17 species of Thalictrum and representatives of related genera in the subfamily Thalictroideae. The plastid-encoded rpl32 gene is likely nonfunctional in members of the subfamily Thalictroideae (Aquilegia, Enemion, Isopyrum, Leptopyrum, Paraquilegia, and Semiaquilegia) including 17 Thalictrum species due to the presence of indels that disrupt the reading frame. A nuclear-encoded rpl32 with high sequence identity was identified in both Thalictrum and Aquilegia. The phylogenetic distribution of this gene loss/transfer and the high level of sequence similarity in transit peptides suggest a single transfer of the plastid-encoded rpl32 to the nucleus in the ancestor of the subfamily Thalictroideae approximately 20-32 Mya. Conclusions: The genome sequence of Thalictrum coreanum provides valuable information for improving the understanding of the evolution of plastid genomes within Ranunculaceae and across angiosperms. Thalictrum is unusual among the three sequenced Ranunculaceae plastid genomes in the loss of two genes infA and rpl32, which have been functionally transferred to the nucleus. In the case of rpl32 this represents the third documented independent transfer from the plastid to the nucleus with the other two transfers occurring in the unrelated angiosperm families Rhizophoraceae and Salicaceae. Furthermore, the transfer of rpl32 provides additional molecular evidence for the monophyly of the subfamily Thalictroideae.
Expression, Crystallization And Preliminary X-Ray Crystallographic Analysis Of Cystathionine Gamma-Synthase (Xometb) From Xanthomonas Oryzae Pv. Oryzae
(2012-12) Ngo, Ho-Phuong-Thuy; Kim, Jin-Kwang; Kim, Seung-Hwan; Pham, Tan-Viet; Tran, Thi-Huyen; Nguyen, Dinh-Duc; Kim, Jeong-Gu; Chung, Sumi; Ahn, Yeh-Jin; Kang, Lin-Woo; Chung, Sumi
Cystathionine gamma-synthase (CGS) catalyzes the first step in the transsulfuration pathway leading to the formation of cystathionine from O-succinylhomoserine and l-cysteine through a gamma-replacement reaction. As an antibacterial drug target against Xanthomonas oryzae pv. oryzae (Xoo), CGS from Xoo (XometB) was cloned, expressed, purified and crystallized. The XometB crystal diffracted to 2.4 angstrom resolution and belonged to the tetragonal space group I4(1), with unit-cell parameters a = b = 165.4, c = 241.7 angstrom. There were four protomers in the asymmetric unit, with a corresponding solvent content of 73.9%.
Functional Activation of ATM by the Prostate Cancer Suppressor NKX3.1
(2013-08) Cai, Bowen W.; Ju, J. H.; Lee, Jeong-Ho; Paull, Tanya T.; Gelmann, Edward P.; Lee, Jeong-Ho; Paull, Tanya T.
The prostate tumor suppressor NKX3.1 augments response to DNA damage and enhances survival after DNA damage. Within minutes of DNA damage, NKX3.1 undergoes phosphorylation at tyrosine 222, which is required for a functional interaction with ataxia telangiectasia mutated (ATM) kinase. NKX3.1 binds to the N-terminal region of ATM, accelerates ATM activation, and hastens the formation of gamma histone2AX. NKX3.1 enhances DNA-dependent ATM kinase activation by both the MRN complex and H2O2 in a DNA-damage-independent manner. ATM, bound to the NKX3.1 homeodomain, phosphorylates NKX3.1, leading to ubiquitination and degradation. Thus, NKX3.1 and ATM have a functional interaction leading to ATM activation and then NKX3.1 degradation in a tightly regulated DNA damage response specific to prostate epithelial cells. These findings demonstrate a mechanism for the tumor-suppressor properties of NKX3.1, demonstrate how NKX3.1 may enhance DNA integrity in prostate stem cells and may help to explain how cells differ in their sensitivity to DNA damage.
Molecular Identification of t(w5): Vps52 Promotes Pluripotential Cell Differentiation Through Cell-Cell Interactions
(2012-11) Sugimoto, Michihiko; Kondo, Masayo; Hirose, Michiko; Suzuki, Misao; Mekada, Kazuyuki; Abe, Takaya; Kiyonari, Hiroshi; Ogura, Atsuo; Takagi, Nobuo; Artzt, Karen; Abe, Kuniya; Artzt, Karen
After implantation, pluripotent epiblasts are converted to embryonic ectoderm through cell-cell interactions that significantly change the transcriptional and epigenetic networks. An entree to understanding this vital developmental transition is the t(w5) mutation of the mouse t complex. This mutation produces highly specific defects in the embryonic ectoderm before gastrulation, leading to death of the embryonic ectoderm. Using a positional cloning approach, we have now identified the mutated gene, completing a decades-long search. The gene, vacuolar protein sorting 52 (Vps52), is a mouse homolog of yeast VPS52 that is involved in the retrograde trafficking of endosomes. Our data suggest that Vps52 acts in extraembryonic tissues to support the growth and differentiation of embryonic ectoderm via cell-cell interactions. It is also required in the formation of embryonic structures at a later stage of development, revealing hitherto unknown functions of Vps52 in the development of a multicellular organism.
NDH Expression Marks Major Transitions in Plant Evolution and Reveals Coordinate Intracellular Gene Loss
(2015-04) Ruhlman, Tracey A.; Chang, Wan-Jung; Chen, Jeremy J. W.; Huang, Yao-Ting; Chan, Ming-Tsair; Zhang, Jin; Liao, De-Chih; Blazier, John C.; Jin, Xiaohua; Shih, Ming-Che; Jansen, Robert K.; Lin, Choun-Sea; Ruhlman, Tracey A.; Zhang, Jin; Blazier, John C.; Jansen, Robert K.
Key innovations have facilitated novel niche utilization, such as the movement of the algal predecessors of land plants into terrestrial habitats where drastic fluctuations in light intensity, ultraviolet radiation and water limitation required a number of adaptations. The NDH (NADH dehydrogenase-like) complex of Viridiplantae plastids participates in adapting the photosynthetic response to environmental stress, suggesting its involvement in the transition to terrestrial habitats. Although relatively rare, the loss or pseudogenization of plastid NDH genes is widely distributed across diverse lineages of photoautotrophic seed plants and mutants/transgenics lacking NDH function demonstrate little difference from wild type under non-stressed conditions. This study analyzes large transcriptomic and genomic datasets to evaluate the persistence and loss of NDH expression across plants. Results: Nuclear expression profiles showed accretion of the NDH gene complement at key transitions in land plant evolution, such as the transition to land and at the base of the angiosperm lineage. While detection of transcripts for a selection of non-NDH, photosynthesis related proteins was independent of the state of NDH, coordinate, lineage-specific loss of plastid NDH genes and expression of nuclear-encoded NDH subunits was documented in Pinaceae, gnetophytes, Orchidaceae and Geraniales confirming the independent and complete loss of NDH in these diverse seed plant taxa. Conclusion: The broad phylogenetic distribution of NDH loss and the subtle phenotypes of mutants suggest that the NDH complex is of limited biological significance in contemporary plants. While NDH activity appears dispensable under favorable conditions, there were likely sufficiently frequent episodes of abiotic stress affecting terrestrial habitats to allow the retention of NDH activity. These findings reveal genetic factors influencing plant/environment interactions in a changing climate through 450 million years of land plant evolution.
Plasticity and Constraints On Fatty Acid Composition in the Phospholipids and Triacylglycerols of Arabidopsis Accessions Grown at Different Temperatures
(2013-04) Sanyal, Anushree; Linder, Craig Randal; Sanyal, Anushree; Linder, Craig Randal
Natural selection acts on multiple traits in an organism, and the final outcome of adaptive evolution may be constrained by the interaction of physiological and functional integration of those traits. Fatty acid composition is an important determinant of seed oil quality. In plants the relative proportions of unsaturated fatty acids in phospholipids and seed triacylglycerols often increases adaptively in response to lower growing temperatures to increase fitness. Previous work produced evidence of genetic constraints between phospholipids and triacylglycerols in the widely studied Arabidopsis lines Col and Ler, but because these lines are highly inbred, the correlations might be spurious. In this study, we grew 84 wild Arabidopsis accessions at two temperatures to show that genetic correlation between the fatty acids of the two lipid types is not expected and one should not influence the other and seed oil evolution and also tested for the adaptive response of fatty acids to latitude and temperature. Results: As expected no significant correlations between the two lipids classes at either growing temperature were observed. The saturated fatty acids and erucic acid of triacylglycerols followed a significant latitudinal cline, while the fatty acids in phospholipids did not respond to latitude as expected. The expected plastic response to temperature was observed for all the triacylglycerol fatty acids whereas only oleic acid showed the expected pattern in phospholipids. Considerable phenotypic variation of the fatty acids in both the lipid types was seen. Conclusion: We report the first evidence supporting adaptive evolution of seed triacylglycerols in Arabidopsis on a latitudinal cline as seen in other species and also their plastic adaptive response to growing temperature. We show that as expected there is no genetic correlations between the fatty acids in triacylglycerols and phospholipids, indicating selection can act on seed triacylglycerols without being constrained by the fatty acid requirements of the phospholipids. Phospholipid fatty acids do not respond to latitude and temperature as seen elsewhere and needs further investigation. Thus, the adaptive response of Arabidopsis and the genetic tools available for manipulating Arabidopsis, makes it an excellent system for studying seed oil evolution and also for breeding seed oil crops especially the Brassica species.
Polyploid Formation Shapes Flowering Plant Diversity
(2014-10) Scarpino, Samuel V.; Levin, Donald A.; Meyers, Lauren A.; Scarpino, Samuel V.; Levin, Donald A.; Meyers, Lauren A.
Polyploidy, or whole genome duplication, has been an important feature of eukaryotic evolution. This is especially true in flowering plants, where all extant angiosperms have descended from polyploid species. Here we present a broad comparative analysis of the effect of polyploidy on flowering plant diversity. We examine the widely held hypothesis that polyploid flowering plants generate more diversity than their diploid counterparts, by fitting stochastic birth/death models to observed ploidal frequency data from 60 extant angiosperm genera. Our results suggest the opposite, that diploids speciate at higher rates than polyploids, through a combination of simple diploid speciation and tetraploidy. Importantly, the estimated diploid advantage stemmed primarily from a higher rate of polyploidization in diploids than polyploids. Our model is also able to account for the empirically observed correlation between polyploidy and species richness without assuming that polyploids have a speciation advantage over diploids.
Sequencing and De Novo Analysis of a Coral Larval Transcriptome Using 454 GSFlx
(2009-05) Meyer, Eli; Aglyamova, Galina V.; Wang, Shi; Buchanan-Carter, Jade; Abrego, David; Colbourne, John K.; Willis, Bette L.; Matz, Mikhail V.; Meyer, Eli; Aglyamova, Galina V.; Wang, Shi; Matz, Mikhail V.
New methods are needed for genomic-scale analysis of emerging model organisms that exemplify important biological questions but lack fully sequenced genomes. For example, there is an urgent need to understand the potential for corals to adapt to climate change, but few molecular resources are available for studying these processes in reef-building corals. To facilitate genomics studies in corals and other non-model systems, we describe methods for transcriptome sequencing using 454, as well as strategies for assembling a useful catalog of genes from the output. We have applied these methods to sequence the transcriptome of planulae larvae from the coral Acropora millepora. Results: More than 600,000 reads produced in a single 454 sequencing run were assembled into similar to 40,000 contigs with five-fold average sequencing coverage. Based on sequence similarity with known proteins, these analyses identified similar to 11,000 different genes expressed in a range of conditions including thermal stress and settlement induction. Assembled sequences were annotated with gene names, conserved domains, and Gene Ontology terms. Targeted searches using these annotations identified the majority of genes associated with essential metabolic pathways and conserved signaling pathways, as well as novel candidate genes for stress-related processes. Comparisons with the genome of the anemone Nematostella vectensis revealed similar to 8,500 pairs of orthologs and similar to 100 candidate coral-specific genes. More than 30,000 SNPs were detected in the coral sequences, and a subset of these validated by re-sequencing. Conclusion: The methods described here for deep sequencing of the transcriptome should be widely applicable to generate catalogs of genes and genetic markers in emerging model organisms. Our data provide the most comprehensive sequence resource currently available for reef-building corals, and include an extensive collection of potential genetic markers for association and population connectivity studies. The characterization of the larval transcriptome for this widely-studied coral will enable research into the biological processes underlying stress responses in corals and evolutionary adaptation to global climate change.
Studies in the Genetics of Drosophila
(University of Texas at Austin, 1940-08-22) University of Texas at Austin
Unique Patterns of Transcript and miRNA Expression in the South American Strong Voltage Electric Eel (Electrophorus Electricus)
(2015-03) Traeger, Lindsay L.; Volkening, Jeremy D.; Moffett, Howell; Gallant, Jason R.; Chen, Po-Hao; Novina, Carl D.; Phillips, George N., Jr.; Anand, Rene; Wells, Gregg B.; Pinch, Matthew; Gueth, Robert; Unguez, Graciela A.; Albert, James S.; Zakon, Harold; Sussman, Michael R.; Samanta, Manoj P.; Zakon, Harold
With its unique ability to produce high-voltage electric discharges in excess of 600 volts, the South American strong voltage electric eel (Electrophorus electricus) has played an important role in the history of science. Remarkably little is understood about the molecular nature of its electric organs. Results: We present an in-depth analysis of the genome of E. electricus, including the transcriptomes of eight mature tissues: brain, spinal cord, kidney, heart, skeletal muscle, Sachs' electric organ, main electric organ, and Hunter's electric organ. A gene set enrichment analysis based on gene ontology reveals enriched functions in all three electric organs related to transmembrane transport, androgen binding, and signaling. This study also represents the first analysis of miRNA in electric fish. It identified a number of miRNAs displaying electric organ-specific expression patterns, including one novel miRNA highly over-expressed in all three electric organs of E. electricus. All three electric organ tissues also express three conserved miRNAs that have been reported to inhibit muscle development in mammals, suggesting that miRNA-dependent regulation of gene expression might play an important role in specifying an electric organ identity from its muscle precursor. These miRNA data were supported using another complete miRNA profile from muscle and electric organ tissues of a second gymnotiform species. Conclusions: Our work on the E. electricus genome and eight tissue-specific gene expression profiles will greatly facilitate future research on determining the coding and regulatory sequences that specify the function, development, and evolution of electric organs. Moreover, these data and future studies will be informed by the first comprehensive analysis of miRNA expression in an electric fish presented here.
Visualizing Science 2015-2016
(The Texas Scientist, 2016) The Texas Scientist