FRY Gene Research Articles

Furry is required for cell movements during gastrulation and functionally interacts with NDR1

Gastrulation is a key event in animal embryogenesis during which germ layer precursors are rearranged and the embryonic axes are established. Cell polarization is essential during gastrulation, driving asymmetric cell division, cell movements, and cell shape changes. The furry (fry) gene encodes an evolutionarily conserved protein with a wide variety of cellular functions, including cell polarization and morphogenesis in invertebrates. However, little is known about its function in vertebrate development. Here, we show that in Xenopus, Fry plays a role in morphogenetic processes during gastrulation, in addition to its previously described function in the regulation of dorsal mesoderm gene expression. Using morpholino knock-down, we demonstrate a distinct role for Fry in blastopore closure and dorsal axis elongation. Loss of Fry function drastically affects the movement and morphological polarization of cells during gastrulation and disrupts dorsal mesoderm convergent extension, responsible for head-to-tail elongation. Finally, we evaluate a functional interaction between Fry and NDR1 kinase, providing evidence of an evolutionarily conserved complex required for morphogenesis.

Fry Is Required for Mammary Gland Development During Pregnant Periods and Affects the Morphology and Growth of Breast Cancer Cells.

The Fry gene, located on chromosome 13, is an evolutionarily conserved large protein from yeast to human. Our previous study genetically linked the Fry gene with differential susceptibility to mammary carcinogenesis, but whether Fry affects mammary gland development and function, as well as the growth of breast cancer cells, is largely unknown. To define the consequences of Fry loss in the mammary glands, we have generated mice conditionally deficient of the Fry gene in the mammary glands using the Cre-loxP recombination system. We examined multiple phenotypes with male and female homozygous Fry conditional knockout mice (Mfry) and control mice (WT), including body weight, preliminary observations (health and neurological flexes), open field locomotion, sensory abilities, auditory threshold, and glucose metabolism. The loss of Fry in the mammary glands didn't cause a significant difference in these genotypes between Mfry and WT mice. However, our data showed that Fry was required during pregnancy, while it was functionally dispensable in virgin mammary gland development. Loss of Fry led to more lateral buds, and the lobuloalveoli were smaller and showed undistended morphology in mammary glands during late pregnancy. in vitro experiment, ectopic expression of FRY could alter the morphology and significantly suppress the growth and proliferation of the breast cancer cell lines, MDA-MB-231 (ER-/PR-/HER2-, Basal-like) and BT474 (ER+/PR+/HER2+, Luminal B). The following genome-wide transcriptomic analysis of these cells suggested that FRY interacted with protein kinases relevant signaling pathways and induced massive changes in gene expression, including the activation of the Hippo/Yap pathway. Together, our data suggest that the FRY is required for mammary glands developments during pregnant periods, and affects breast cancer cell growth and proliferation.

A Novel Homozygous Deletion within the FRY Gene Associated with Nonsyndromic Developmental Delay

The role of autosomal recessive (AR) variants in clinically heterogeneous conditions such as intellectual disability and developmental delay (ID/DD) has been difficult to uncover. Implication of causative pathogenic AR variants often requires investigation within large and consanguineous families, and/or identifying rare biallelic variants in affected individuals. Furthermore, detection of homozygous gene-level copy number variants during first-line genomic microarray testing in the pediatric population is a rare finding. We describe a 6.7-year-old male patient with ID/DD and a novel homozygous deletion involving the FRY gene identified by genomic SNP microarray. This deletion was observed within a large region of homozygosity on the long arm of chromosome 13 and in a background of increased low-level (2.6%) autosomal homozygosity, consistent with a reported common ancestry in the family. FRY encodes a protein that regulates cell cytoskeletal dynamics, functions in chromosomal alignment in mitosis in vitro, and has been shown to function in the nervous system in vivo. Homozygous mutation of FRY has been previously reported in 2 consanguineous families from studies of autosomal recessive ID in Middle Eastern and Northern African populations. This report provides additional supportive evidence that deleterious biallelic mutation of FRY is associated with ID/DD and illustrates the utility of genomic SNP microarray detection of low-level homozygosity.

EXPRESSION ANALYSIS OF THE COFFE (Coffea arabica L.) FRIGIDA4-like GENE (CaFRL4)

ABSTRACT
 Coffee is one of the most economically important commodities. In Brazil, this crop is responsible for generating more than eight million jobs. In the foreign market, Brazil is the largest producer and exporter of coffee. Due to its economic importance, several studies aiming the improvement of coffee are conducted, but there are still problems related to its productivity and quality of the beverage, such as sequential flowering, which causes production losses and a low quality drink. Thus, understanding the molecular mechanisms involved in the flowering process is essential to elucidate how flowering occurs in the coffee crop. The FRI gene is one of the main genes involved in flowering, as it positively regulates the FLC gene at expression levels that inhibit flowering. Thus, the objective of this work was to identify and analyze the expression of the FRIGIDA4-like gene (FRL4) through Bioinformatics and real-time PCR (RT-qPCR). The CaFRL4 gene was identified and showed high expression levels in leaf during flowering, which corroborates with the literature. The results obtained provide the basis for future studies involving genetic transformation in model plants and coffee, permitting the functional characterization of this gene.

Fryl deficiency is associated with defective kidney development and function in mice.

FRY like transcription coactivator ( Fryl) gene located on chromosome 5 is a paralog of FRY microtubule binding protein ( Fry) in vertebrates. It encodes a protein with unknown functions. Fryl gene is conserved in various species ranging from eukaryotes to human. Although there are several reports on functions of Fry gene, functions of Fryl gene remain unclear. A mouse line containing null mutation in Fryl gene by gene trapping was produced in this study for the first time. The survival and growth of Fryl-/- mice were observed. Fryl gene expression levels in mouse tissues were determined and histopathologic analyses were conducted. Most Fryl-/- mice died soon after birth. Rare Fryl-/- survivors showed growth retardation with significantly lower body weight compared to their littermate controls. Although they could breed, more than half of Fryl-/- survivors died of hydronephrosis before age 1. No abnormal histopathologic lesion was apparent in full-term embryo or adult tissues except the kidney. Abnormal lining cell layer detachments from walls of collecting and convoluted tubules in kidneys were apparent in Fryl-/- neonates and full-term embryos. Fryl gene was expressed in renal tubular tissues including the glomeruli and convoluted and collecting tubules. This indicates that defects in tubular systems are associated with Fryl functions and death of Fryl-/- neonates. Fryl protein is required for normal development and functional maintenance of kidney in mice. This is the first report of in vivo Fryl gene functions. Impact statement FRY like transcription coactivator ( Fryl) gene is conserved in various species ranging from eukaryotes to human. It expresses a protein with unknown function. We generated a Fryl gene mutant mouse line and found that most homozygous mice died soon after their birth. Rare Fryl-/- survivors showed growth retardation with significantly lower body weight compared to their littermate controls. Although they could breed, more than half of Fryl-/- survivors died of hydronephrosis before age 1. Full-term mutant embryos showed abnormal collecting and convoluted tubules in kidneys where Fryl gene was expressed. Collectively, these results indicate that Fryl protein is required for normal development and functional maintenance of kidney in mice. To the best of our knowledge, this is the first report on in vivo Fryl gene functions.

Abstract 1160: FRY Inhibits progression and metastasis of breast cancer through activating Hippo signaling pathway

Abstract Background: Recently, we reported that using quantitative trait locus (QTL) mapping in differentially susceptible rat strains, we identified Fry, the mammalian ortholog of the furry gene in Drosophila melanoganster, as a candidate mammary carcinoma susceptibility gene (Mcs30). Preliminary studies of rat Fry gene suggest that Fry may play a key role in epithelial-mesenchymal transition (EMT), tumor progression and metastasis. Methods: In the present study, we modified and established multiple breast cancer cell lines with enhanced expression of either wildtype or mutated human FRY gene. We examined the anti-tumorigenic and anti-metastatic effects of enhanced FRY expression on these cell lines in vitro and in vivo. We also utilized RNA-seq and proteomic approach to dissect FRY-regulated signaling molecules and pathways. Results: Ectopic expression of wild-type FRY significantly diminished tumorigenicity and metastasis of breast cancer cells both in vitro and in animal studies, particularly in the triple negative breast cancer cell line, MDA-MB-231 cells. Relative to the rapidly tumors growth of MDA-MB-231 cells in vitro and in nude mice assay, the growth of MDA-MB-231 cells ectopically expressing the FRY significantly reduced. In comparison, the anti-tumorigenic effects of mutated FRY were compromised but remained significant. Further, we showed that FRY's effects in suppressing proliferation, invasion, and metastasis of breast cancer cells were partially through the activation of Hippo signaling pathway. Conclusions: These results provide direct evidence in supporting the important role of FRY in breast cancer progression and metastasis, and first time reveal a connection between FRY and the Hippo signaling pathway. Citation Format: Hao Zhang, Fan Fei, Xushen Chen, Zi Ceng, Xiaojiang Tang, Helmut Zarbl, Xuefeng Ren. FRY Inhibits progression and metastasis of breast cancer through activating Hippo signaling pathway. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1160.

Sa1456 The Methylation at cg 16941656 of FRY Gene in Bile as a Biomarker for Pancreatic Cancer

Sa1456 The Methylation at cg 16941656 of FRY Gene in Bile as a Biomarker for Pancreatic Cancer

Abstract A20: Decreased nuclear expression of the FRY protein identifies a subset of breast cancers with poor clinical outcomes

Abstract The goal of the present study was to determine if decreased nuclear expression of the human FRY protein can serve as a biomaker of breast cancer progression and outcomes. We previously identified the rat Fry gene as a putative mammary carcinoma susceptibility (Mcs) gene. We further demonstrated that FRY expression was decreased in several human breast cancer cell lines. Moreover, ectopic expression of wildtype Fry suppressed tumorigenicity of the triple negative MDA-MD-231 breast cancer cells in vitro and in vivo by promoting epithelial cell differentiation. To evaluate the contribution of altered FRY expression to the clinical progression of human breast cancer, we first compared FRY mRNA expression in >4,800 clinically annotated human breast cancers using DNA microarray data from 19 distinct cohorts available from the Oncomine 3.0 Cancer Profiling Database. The analysis indicated that decreased FRY mRNA was significantly correlated with poorly differentiated tumor histopathology, increased Elston tumor grade, and triple negative status (loss of estrogen, progesterone and Her2 receptors). Using commercially available breast cancer tissue microarrays, we used semi-quantitative immunohistochemistry and quantitative image analysis to compare FRY protein expression in normal mammary tissue and tumors. The results indicated that loss of FRY expression was a frequent event during progression of mammary carcinomas. We therefore analyzed >1200 clinically annotated breast cancers represented on tissue microarrays from commercial suppliers and the National Cancer Institute (NCI) Cancer Diagnosis Program, including the Breast Cancer Diagnosis and Progression panels. FRY protein expression was evaluated by immunohistochemical staining and was graded on a scale of 0 to 4 (0, +, ++, +++, ++++). The analysis indicated that decreased nuclear expression of the FRY protein was significantly correlated with poorly differentiated histopathologies, increasing Elston grade and loss of the estrogen receptor. Tumors with decreased FRY expression were also more likely to metastasize and were associated with decreased tumor-free survival. These findings indicated that loss of nuclear FRY expression identifies a subset of breast cancer with poor clinical outcomes, suggesting that FRY may serve as an early biomarker for breast cancer progression and prognosis. Citation Format: Helmut Zarbl, Jessica C. Graham, Norio Takizawa, Mingzhu Fang, Zhihong Gong, Brian Estrella, Xuefeng Ren. Decreased nuclear expression of the FRY protein identifies a subset of breast cancers with poor clinical outcomes. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research; Oct 17-20, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(2_Suppl):Abstract nr A20.

Recurrent fusion transcripts detected by whole-transcriptome sequencing of 120 primary breast cancer samples.

Relatively few recurrent gene fusion events have been associated with breast cancer to date. In an effort to uncover novel fusion transcripts, we performed whole-transcriptome sequencing of 120 fresh-frozen primary breast cancer samples and five adjacent normal breast tissues using the Illumina HiSeq2000 platform. Three different fusion-detecting tools (deFuse, Chimerascan, and TopHatFusion) were used, and the results were compared. These tools detected 3,831, 6,630 and 516 fusion transcripts (FTs) overall. We primarily focused on the results obtained using the deFuse software. More FTs were identified from HER2 subtype breast cancer samples than from the luminal or triple-negative subtypes (P < 0.05). Seventy fusion candidates were selected for validation, and 32 (45.7%) were confirmed by RT-PCR and Sanger sequencing. Of the validated fusions, six were recurrent (found in 2 or more samples), three were in-frame (PRDX1-AKR1A1, TACSTD2-OMA1, and C2CD2-TFF1) and three were off-frame (CEACAM7-CEACAM6, CYP4X1-CYP4Z2P, and EEF1DP3-FRY). Notably, the novel read-through fusion, EEF1DP3-FRY, was identified and validated in 6.7% (8/120) of the breast cancer samples. This off-frame fusion results in early truncation of the FRY gene, which plays a key role in the structural integrity during mitosis. Three previously reported fusions, PPP1R1B-STARD3, MFGE8-HAPL, and ETV6-NTRK3, were detected in 8.3, 3.3, and 0.8% of the 120 samples, respectively, by both deFuse and Chimerascan. The recently reported MAGI3-AKT3 fusion was not detected in our analysis. Although future work will be needed to examine the biological significance of our new findings, we identified a number of novel fusions and confirmed some previously reported fusions.

Mapping of Mcs30, a New Mammary Carcinoma Susceptibility Quantitative Trait Locus (QTL30) on Rat Chromosome 12: Identification of Fry as a Candidate Mcs Gene

Rat strains differ dramatically in their susceptibility to mammary carcinogenesis. On the assumption that susceptibility genes are conserved across mammalian species and hence inform human carcinogenesis, numerous investigators have used genetic linkage studies in rats to identify genes responsible for differential susceptibility to carcinogenesis. Using a genetic backcross between the resistant Copenhagen (Cop) and susceptible Fischer 344 (F344) strains, we mapped a novel mammary carcinoma susceptibility (Mcs30) locus to the centromeric region on chromosome 12 (LOD score of ∼8.6 at the D12Rat59 marker). The Mcs30 locus comprises approximately 12 Mbp on the long arm of rat RNO12 whose synteny is conserved on human chromosome 13q12 to 13q13. After analyzing numerous genes comprising this locus, we identified Fry, the rat ortholog of the furry gene of Drosophila melanogaster, as a candidate Mcs gene. We cloned and determined the complete nucleotide sequence of the 13 kbp Fry mRNA. Sequence analysis indicated that the Fry gene was highly conserved across evolution, with 90% similarity of the predicted amino acid sequence among eutherian mammals. Comparison of the Fry sequence in the Cop and F344 strains identified two non-synonymous single nucleotide polymorphisms (SNPs), one of which creates a putative, de novo phosphorylation site. Further analysis showed that the expression of the Fry gene is reduced in a majority of rat mammary tumors. Our results also suggested that FRY activity was reduced in human breast carcinoma cell lines as a result of reduced levels or mutation. This study is the first to identify the Fry gene as a candidate Mcs gene. Our data suggest that the SNPs within the Fry gene contribute to the genetic susceptibility of the F344 rat strain to mammary carcinogenesis. These results provide the foundation for analyzing the role of the human FRY gene in cancer susceptibility and progression.

Genetic base of Arabidopsis thaliana (L.) Heynh: fitness of plants for extreme conditions in northern margins of species range

Flowering time and vernalization requirement were studied in eight natural Karelian populations (KPs) of Arabidopsis thaliana. These KPs consisted of late-flowering plants with elevated expression of flowering repressor FLC and a reduced expression level of flowering activator SOC1 compared to the early-flowering ecotypes Dijon-M and Cvi-0. Despite variations in flowering time and the vernalization requirement among the KPs, two-week-old seedlings showed no changes in either the nucleotide sequence of the FRI gene or the relative expression levels of FRI and its target gene FLC that would be responsible for this variation. An analysis of abscisic acid (ABA) biosynthesis and catabolism genes (NCED3 and CYP707A2) did not show significant differences between late-flowering KPs and the early-flowering ecotypes Dijon-M and Cvi-0. Cold treatment (4 degrees C for 24 h) induced the expression of not only NCED3, but also RD29B, a gene involved in the ABA-dependent cold-response pathway. The relative levels of cold activation of these genes were nearly equal in all genotypes under study. Thus, the ABA-dependent cold response pathway does not depend on FLC expression. The lack of significant differences between northern populations, as well as the ecotypes Dijon-M (Europe) and Cvi-0 (Cape Verde Islands), indicates that this pathway is not crucial for fitness to the northern environment.

Abstract LB-131: Decreased nuclear localization and expression of the FRY tumor suppressor gene, a repressor of epithelial mesenchymal transition, are highly correlated with breast cancer phenotype, grade, and progression

Abstract Using Quantitative Trait Locus (QTL) mapping in a backcross between susceptible Fischer 344 and resistant Copenhagen rat strains, we identified Fry, the rat ortholog of the Drosophila melanoganster furry gene, as a mammary carcinoma susceptibility (Mcs) gene. The Fischer 344 Fry allele harbors two single nucleotide polymorphisms that alter amino acid residues that are highly conserved from yeast to humans. One of these SNPs replaces an Alanine with a Serine residue, creating a de novo concensus sequence for several cancer-associated protein kinases. In the lower eucaryoyes, the furry orthologs are implicated in diverse cell processes including epithelial cell polarization, morphogenesis, proliferation, cytokinesis, and regulation of the NDR family of kinases, some of which are putative human tumor suppressor genes. Consistent with its function as a tumor suppressor gene, ectopic expression of the FRY gene was reduced in 3 of 4 human breast cancer cell lines. Ectopic expression of the wildtype allele significantly reduced the tumorigenicity of the human MDA-MB-231 mammary carcinoma cell line. In contrast to the parental MDA-MB-231 cells, which grew randomly in Matrigel® matrix, those expressing Fry (231CFry) formed spherical colonies of differentiated cells, closely resembling those formed by MCF-10A normal mammary epithelial cell line. When xenographed into nude mice, the 231CFry cells demonstrated a dramatic reduction in tumorigenicity (8x reduction in tumor volume at 15 days) and diminished invasiveness into surrounding tissues. Gene expression profiling suggested that in MDA-MB-231 cells, ectopic Fry induced the expression of gene networks involved in cell differentiation, proliferation, and polarization, consistent with a role for FRY in suppressing epithelial-mesenchymal transition (EMT). To investigate the role of human FRY in breast cancer, we examined FRY mRNA expression in &amp;gt;1,500 human breast cancers, representing distinct eight cohorts entered into the Oncomine 3.0 Cancer Profiling Database. Our analysis revealed that decreased FRY mRNA was highly correlated with poorly differentiated breast cancer phenotypes (p&amp;lt;0.0001), increasing Elston tumor grade (p&amp;lt;0.0001) and clinically aggressive cancer phenotypes (p&amp;lt;0.05). Using an anti-FRY peptide antiserum, we examined FRY protein expression in cores comprising the BR208 breast cancer and tissue microarrays from US Biomax, Inc. Immunohistochemical staining patterns were analyzed by quantitative image analysis software and independently by a board certified pathologist. The analyses indicated that decreased nuclear localization and expression of FRY were highly correlated with histopathology, clinical grade and progression, indicating that the FRY tumor suppressor is an important new biomarkers of breast cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-131. doi:10.1158/1538-7445.AM2011-LB-131

Gene Expression and Ex Vivo Drug Sensitivity Profiles in Children with Acute Leukemia: An Insight for High-Dose Therapy and Role of Etoposide and Fludarabine.

Abstract 2747Poster Board II-723 Background:A distinct phenotype of combined ex vivo drug resistance and gene expression associated with this phenotype discriminates treatment outcome and identifies a subset of patients with a markedly inferior outcome in childhood acute lymphoblastic leukemia (ALL). No similar relationship was found so far in acute myeloblastic leukemia (AML). We hypothesized that drug sensitivity profile combined with gene expression profile can provide a new insight into selection of drugs used in high-dose therapy before hematopoietic stem cell transplantation and determine the role of specific drugs. Objective:The aim of the study was to analyze the gene expression profile in correlation to the ex vivo obtained chemosensitivity profile of drugs used in high-dose therapy before hematopoietic stem cell transplantation in children with ALL and AML. Methods:We tested leukemic cells from 56 children (43 ALL de novo, 8 relapsed ALL, 5 AML de novo) for ex vivo sensitivity to etoposide, fludarabine, 4-HOO-cyclophosphamide, busulfan, treosulfan and melphalan. The cells were then subjected to an assessment of global profile of gene expression to identify differentially expressed genes in drug-sensitive and drug-resistant ALL. Cells were isolated from bone marrow at the initial diagnosis of leukemia or its relapse. In vitro cytotoxicity was analyzed by means of the MTT assay. The drug resistance was expressed as the IC50, the inhibitory concentration to 50% of the cells. RNA was extracted with the use of Trizol, purified and assessed for integrity. Samples were hybridized to the Human Genome U133A Chip oligonucleotide microarrays (Affymetrix) according to manufacturer's protocol. Dataset was pre-processed by RMA method and small variability genes were filtered out. The final analysis was carried out in 13 835 probe sets. Non-parametric Spearman's correlations of IC50 and gene expression values were analyzed. Results:From all analyzed drugs, the largest number of genes significantly associated with the chemosensitivity profile across samples was observed for etoposide. We found 386 probests significantly correlated with the IC50 values (Spearman's correlation coefficient ranging from R==0.7 to R=0.61, p<0.001). NUDT21 gene (Nudix, nucleoside diphosphate linked moiety X-type, motif 21) was found to be highly significantly (False Discovery Rate, FDR<0.0001%) associated with chemosensitivity (larger expression associated with decreased IC50). Global test of association confirmed (p<0.001) that overall gene expression profile is associated with etoposide resistance, among selected genes there was over-representation of transcripts from chromosomes 1, 16 and 19. Two other drugs were found to exhibit noticeable association: fludarabine chemosensitivity was correlated with the expression of 197 probesets, global test of significance p=0.002; for cyclophosphamide 111 probesets and p=0.006 in global test was obtained. Much less significant association was observed for melphalan (72 genes, global test p=0.02) and almost no association was found for treosulfan (28 probesets, global test p=0.12) and busulfan (22 probesets, global test p=0.18). Fludarabine resistance was associated with an increased expression of FRY gene (Drosophila Furry homolog), Spearman's correlation coefficient R=0.61 (FDR=0.27%). Melphalan sensitivity was associated with biologically interesting differences in gene expression of PIP4K2A (Phosphatidyloinositol-5-phosphate 4-kinase, type II, alpha; over-expressed in patients with high IC50 for this drug) and POLR2C (RNA Polymerase II, DNA directed, polypeptide C, 33 kDa; down-regulated in this subset of cases). Conclusions:Expression of a single genes is strongly associated with drug resistance in childhood acute leukemia, and it may aid to determine drug sensitivity to high-dose chemotherapy. Etoposide and fludarabine sensitivity seem to be related to the significant number of biologically important genes. Acknowledgments:This study was supported by grants MNiSW N407 078 32/2964 and UMK BW 10/09. JSz and MJ contributed equally to the study. Disclosures:No relevant conflicts of interest to declare.

Candidate Gene Association Mapping of Arabidopsis Flowering Time

The pathways responsible for flowering time in Arabidopsis thaliana comprise one of the best characterized genetic networks in plants. We harness this extensive molecular genetic knowledge to identify potential flowering time quantitative trait genes (QTGs) through candidate gene association mapping using 51 flowering time loci. We genotyped common single nucleotide polymorphisms (SNPs) at these genes in 275 A. thaliana accessions that were also phenotyped for flowering time and rosette leaf number in long and short days. Using structured association techniques, we find that haplotype-tagging SNPs in 27 flowering time genes show significant associations in various trait/environment combinations. After correction for multiple testing, between 2 and 10 genes remain significantly associated with flowering time, with CO arguably possessing the most promising associations. We also genotyped a subset of these flowering time gene SNPs in an independent recombinant inbred line population derived from the intercrossing of 19 accessions. Approximately one-third of significant polymorphisms that were associated with flowering time in the accessions and genotyped in the outbred population were replicated in both mapping populations, including SNPs at the CO, FLC, VIN3, PHYD, and GA1 loci, and coding region deletions at the FRI gene. We conservatively estimate that approximately 4-14% of known flowering time genes may harbor common alleles that contribute to natural variation in this life history trait.

Population Genomics of the Arabidopsis thaliana Flowering Time Gene Network

The time to flowering is a key component of the life-history strategy of the model plant Arabidopsis thaliana that varies quantitatively among genotypes. A significant problem for evolutionary and ecological genetics is to understand how natural selection may operate on this ecologically significant trait. Here, we conduct a population genomic study of resequencing data from 52 genes in the flowering time network. McDonald-Kreitman tests of neutrality suggested a strong excess of amino acid polymorphism when pooling across loci. This excess of replacement polymorphism across the flowering time network and a skewed derived frequency spectrum toward rare alleles for both replacement and noncoding polymorphisms relative to synonymous changes is consistent with a large class of deleterious polymorphisms segregating in these genes. Assuming selective neutrality of synonymous changes, we estimate that approximately 30% of amino acid polymorphisms are deleterious. Evidence of adaptive substitution is less prominent in our analysis. The photoperiod regulatory gene, CO, and a gibberellic acid transcription factor, AtMYB33, show evidence of adaptive fixation of amino acid mutations. A test for extended haplotypes revealed no examples of flowering time alleles with haplotypes comparable in length to those associated with the null fri(Col) allele reported previously. This suggests that the FRI gene likely has a uniquely intense or recent history of selection among the flowering time genes considered here. Although there is some evidence for adaptive evolution in these life-history genes, it appears that slightly deleterious polymorphisms are a major component of natural molecular variation in the flowering time network of A. thaliana.

Listeria monocytogenes ferritin protects against multiple stresses and is required for virulence

In this study, the role of Listeria monocytogenes ferritin was investigated. The fri gene encoding the ferritin was deleted and the phenotype of the mutant was analyzed demonstrating that ferritin is necessary for optimal growth in minimal medium in both presence and absence of iron, as well as after cold- and heat-shock. We also showed that ferritin provides protection against reactive oxygen species and is essential for full virulence of L. monocytogenes. A comparative proteomic analysis revealed an effect of the fri deletion on the levels of listeriolysin O and several stress proteins. Together, our study demonstrates that fri has multiple roles that contribute to Listeria virulence.

The Dps-like protein Fri of Listeria monocytogenes promotes stress tolerance and intracellular multiplication in macrophage-like cells

Members of the ferritin-like Dps protein family are found in a number of bacterial species, where they demonstrate the potential to bind iron, and have been implicated in tolerance to oxidative stress. In this study of the food-borne pathogen Listeria monocytogenes, the fri gene encoding a Dps homologue was deleted, and, compared to wild-type cells, it was found that the resulting mutant was less resistant to hydrogen peroxide, and demonstrated reduced survival following long-term (7-11 days) incubation in laboratory media. In view of this, it is shown that fri gene expression is controlled by the hydrogen peroxide regulator PerR, as well as the general stress sigma factor sigmaB. When fri mutant cells were transferred to iron-limiting conditions, growth was retarded relative to wild-type cells, indicating that Fri may be required for iron storage. This notion is supported by the observation that the L. monocytogenes genome appears not to encode other ferritin-like proteins. Given the role of Fri in resistance to oxidative stress, and growth under iron-limiting conditions, the ability of the fri mutant to infect mice was examined. When injected by the intraperitoneal route, the fri mutant demonstrated a reduced capacity to proliferate in the organs of infected mice relative to the wild-type, whereas when the bacteria were supplied intravenously this effect was mitigated. In addition, the mutant was impaired in its ability to survive and grow in J774.A1 mouse macrophage cells. Thus, the data suggest that Fri contributes to the ability of L. monocytogenes to survive in environments where oxidative stress and low iron availability may impede bacterial proliferation.

Haplotype Structure and Phenotypic Associations in the Chromosomal Regions Surrounding Two Arabidopsis thaliana Flowering Time LociSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AY781906, AY785055.

The feasibility of using linkage disequilbrium (LD) to fine-map loci underlying natural variation in Arabidopsis thaliana was investigated by looking for associations between flowering time and marker polymorphism in the genomic regions containing two candidate genes, FRI and FLC, both of which are known to contribute to natural variation in flowering. A sample of 196 accessions was used, and polymorphism was assessed by sequencing a total of 17 roughly 500-bp fragments. Using a novel Bayesian algorithm based on haplotype similarity, we demonstrate that LD could have been used to fine-map the FRI gene to a roughly 30-kb region and to identify two common loss-of-function alleles. Interestingly, because of genetic heterogeneity, simple single-marker associations would not have been able to map FRI with nearly the same precision. No clear evidence for previously unknown alleles at either locus was found, but the effect of population structure in causing false positives was evident.