Ritesh Mewalal

Lawrence Berkeley National Laboratory | LBL · Environmental Genomics & Systems Biology

During symbiosis, organisms use a range of metabolic and protein-based signals to communicate. Of these protein signals, one class is defined as ‘effectors’, i.e., small secreted proteins (SSPs) that cause phenotypical and physiological changes in another organism. To date, protein-based effectors have been described in aphids, nematodes, fungi and...

Research toward renewable and sustainable energy has identified specific terpenes capable of supplementing or replacing current petroleum-derived fuels. Despite being naturally produced and stored by many plants, there are few examples of commercial recovery of terpenes from plants because of low yields. Plant terpene biosynthesis is regulated at m...

DUF1218 is a land plant-specific innovation and has previously been shown to be associated with cell wall biology, vasculature patterning and abiotic/biotic stress response. The Arabidopsis genome encodes 15 members, two of which (At1g31720 and At4g27435) are preferentially expressed in the secondary cell wall depositing inflorescence stems. To fur...

Plant biomass, as an abundant renewable carbon source, is a promising alternative to fossil fuels. However, the enzymes most commonly used for depolymerization of lignocellulosic biomass are expensive, and the development of cost-effective alternative conversion technologies would be desirable. One possible option is the heterologous expression of...

Lignocellulosic biomass is an important feedstock for the pulp and paper industry as well as emerging biofuels and biomaterials industries. However, recalcitrance of the secondary cell wall to chemical or enzymatic degradation remains a major hurdle for efficient extraction of economically important biopolymers such as cellulose. It has been estima...

The molecular mechanisms underlying mycorrhizal symbioses, the most ubiquitous and impactful mutualistic plant–microbial interaction in nature, are largely unknown. Through genetic mapping, resequencing and molecular validation, we demonstrate that a G-type lectin receptor-like kinase (lecRLK) mediates the symbiotic interaction between Populus and...

Ecto- and endo-mycorrhizal colonization of Populus roots have a positive impact on the overall tree health and growth.A complete molecular understanding of these interactions will have important implications for increasing agricultural or forestry sustainability using plant: microbe-based strategies. These beneficial associations entail extensive m...

Crassulacean acid metabolism (CAM) improves photosynthetic efficiency under limited water availability relative to C3 photosynthesis. It is widely accepted that CAM plants have evolved from C3 plants and it is hypothesized that CAM is under the control of the internal circadian clock. However, the role that the circadian clock plays in the evolutio...

A characteristic feature of plant cells is the ability to form callus from parenchyma cells in response to biotic and abiotic stimuli. Tissue culture propagation of recalcitrant plant species and genetic engineering for desired phenotypes typically depends on efficient in vitro callus generation. Callus formation is under genetic regulation, and co...

Negatively co-expressed genes between Potri.006G222700, a gene of unknown function, and Potri.008G208200, a RALF-LIKE protein 22. (XLSX)

Negatively co-expressed genes between Potri.006G222700, a gene of unknown function, and Potri.012G083800, a RPD3 histone deacetylase protein. (XLSX)

Co-expressed genes between Potri.004G118700, a targeting protein for XKLP2, Potri.015G023600, a gene of unknown function, and Potri.018G014800, CNDbr, Chloroplast Nucleoid DNA-binding-related gene. (XLSX)

Co-expressed genes between Potri.003G018500, a SOK1 kinase, and Potri.012G083800, a RPD3 histone deacetylase protein. (XLSX)

Negatively co-expressed genes between Potri.004G118700, a targeting protein for XKLP2, and Potri.015G023600, a gene of unknown function. (XLSX)

Tissue and organ expression patterns of four callus formation genes and four callus rating score genes. Data was obtained from Phytozome 11.0 (Goodstein et al. 2012) and depicted as log2(FPKM). (DOCX)

Heat map of differentially expressed Arabidopsis orthologs, over 96 hours during callus induction, for Populus genes associated with callus formation or callus score in a genome-wide association study. Data taken from: www.ncbi.nlm.nig.gov/geo/ (Fan et al. 2012). (DOCX)

Co-expression network for orthologs of Arabidopsis genes tested in transgenic experiments and their association with Populus callus formation and callus rating genes identified via genome-wide association approaches. Arabidopsis orthologs are presented in parenthesis and Populus candidate genes are underlined. The Populus genes were discovered usin...

Chromosome location for single nucleotide polymorphisms associations with Populus callus phenotypes that exceeded a Bonferroni-adjusted significance threshold [p = 3.47E−05]. (XLSX)

qRT-PCR primers used in the transient protoplast assay. (XLSX)

Co-expressed genes between Potri.009G066100, a mitogen-activated protein kinase, and Potri.018G014800, CNDbr, a Chloroplast Nucleoid DNA-binding-related gene. (XLSX)

Crassulacean acid metabolism (CAM) is a water-use efficient adaptation of photosynthesis that has evolved independently many times in diverse lineages of flowering plants. We hypothesize that convergent evolution of protein sequence and temporal gene expression underpins the independent emergences of CAM from C 3 photosynthesis. To test this hypoth...

Non-coding RNAs (ncRNAs), that is, RNAs not translated into proteins, are crucial regulators of a variety of biological processes in plants. While protein-encoding genes have been relatively well-annotated in sequenced genomes, accounting for a small portion of the genome space in plants, the universe of plant ncRNAs is rapidly expanding. Recent ad...

Gene ontology enrichment of MWL-1 top 300 co-expressed genes in Arabidopsis. Co-expressed genes were extracted from ATTED-II [10]. GO-full was conducted in Cytoscape 2.8.2 [22] using BiNGO 2.44 [21], while overrepresentation summary enrichment was performed with the REVIGO server [23]. (DOCX)

Phenotypic analysis of At1g31720 (MWL-1) single T-DNA knockout line mutants and MWL-1 overexpression lines. (A) RT-PCR detection of endogenous MWL-1 transcript in the wildtype (WT) plants and absence in the single knockout mutant. (B) Semi-quantitative RT-PCR analysis of MWL-1 overexpression lines 1 to 3 showing detection of MWL-1 transgene in the...

Phylogenetic and bioinformatics analysis of all members of the Arabidopsis domain of unknown function 1218 (DUF1218) family, and expression profiling of the candidate members, MODIFYING WALL LIGNIN-1 (MWL-1, At1g31720) and MWL-2 (At4g19370). (A) Neighbor-joining phylogenetic tree of Arabdiopsis DUF1218-containing proteins. ClustalW was used to alig...

Phenotypic analysis of At4g19370 (MWL-2) single T-DNA knockout line mutants and MWL-2 overexpression lines. (A) RT-PCR detection of endogenous MWL-2 transcript in the wildtype (WT) plants and absence in the single knockout mutant. (B) Semi-quantitative RT-PCR analysis of MWL-2 overexpression lines 1 to 3 showing detection of MWL-2 transgene in the...