Project description:Deciphering the various chemical modifications of both DNA and the histone compound of chromatin not only leads to a better understanding of the genome-wide organization of epigenetic landmarks and their impact on gene expression but may also provide some insights into the evolutionary processes. Although both histone modifications and DNA methylation have been widely investigated in various plant genomes, here we present the first study for the genus Lupinus. Lupins, which are members of grain legumes (pulses), are beneficial for food security, nutrition, health and the environment. In order gain a better understanding of the epigenetic organization of genomes in lupins we applied the immunostaining of methylated histone H3 and DNA methylation as well as whole-genome bisulfite sequencing. We revealed variations in the patterns of chromatin modifications at the chromosomal level among three crop lupins, i.e. L. angustifolius (2n=40), L. albus (2n=50) and L. luteus (2n=52), and the legume model plant Medicago truncatula (2n=16). Different chromosomal patterns were found depending on the specific modification, e.g. H3K4me2 was localised in the terminal parts of L. angustifolius and M. truncatula chromosomes, which is in agreement with the results that have been obtained for other species. Interestingly, in L. albus and L. luteus this modification was limited to one arm in the case of all of the chromosomes in the complement. Additionally, H3K9me2 was detected in all of the analysed species except L. luteus. DNA methylation sequencing (CG, CHG and CHH contexts) of aforementioned crop but also wild lupins such as L. cosentinii (2n=32), L. digitatus (2n=36), L. micranthus (2n=52) and L. pilosus (2n=42) supported the range of interspecific diversity. The examples of epigenetic modifications illustrate the diversity of lupin genomes and could be helpful for elucidating further epigenetic changes in the evolution of the lupin genome.
Project description:Investigation of transcriptomic changes in M.luteus at 12hrs and 24hrs. Differences in fatty acid profiles of M. luteus at exponential and stationary phase is attributed to transcriptional changes of branched amino acid biosynthesis and degradation genes. This study is described by Pereira, J.H., E.B. Goh, J.D. Keasling, H.R. Beller and P.A. Adams in Crystal structure of FabH and factors affecting the distribution of branched fatty acids in Micrococcus luteus, which has been submitted to Acta Crystallographica Section D A 6 microarray study using total RNA recovered from six separate control cultures of Micrococcus luteus NCTC2665 strain with 3 harvested after 12hrs of growth and the other 3 after 24hrs of growth. Each chip measures the expression level of 2,374 ORF based on the draft genome sequence of Micrococcus luteus with ten 60-mer probe pairs (PM/MM) per gene, with 3-fold technical redundancy.
Project description:Illumina HiSeq technology was used to generate mRNA profiles from Suillus luteus ectomycorrhizal roots compared to free-living mycelium . Mycorrhizal roots were harvested after 40 days, pooled and used for RNA extraction. Reads of 2X100bp were generated and aligned to Suillus luteus (http://genome.jgi-psf.org/Suilu1/Suilu1.home.html) using CLC Genomics Workbench 6.
Project description:Illumina HiSeq technology was used to generate mRNA profiles from Suillus luteus ectomycorrhizal roots compared to free-living mycelium . Mycorrhizal roots were harvested after 40 days, pooled and used for RNA extraction. Reads of 2X100bp were generated and aligned to Suillus luteus (http://genome.jgi-psf.org/Suilu1/Suilu1.home.html) using CLC Genomics Workbench 6. mRNA profiles from Suillus luteus ectomycorrhizal roots and free-living mycelium were generated by paired-end (2x100bp) Illumina HiSeq2000 sequencing. Two biological replicates were sequenced for mycorrhizal and mycelium samples.
Project description:Investigation of whole genome gene expression level changes in a E. coli fatty acid overproducing strain with or without heterologous expression of the M. luteus FabH. The strain expressing M. luteus FabH produces more methyl ketones. This study will be further described in Goh, E.B., E.E.K. Baidoo, J.D. Keasling, and H.R. Beller. Engineering of bacterial methyl ketone synthesis for biofuels.
