A5073914365- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Microbial Metabolic Engineering and Bioproduction
- Photosynthetic Processes and Mechanisms
- Plant tissue culture and regeneration
- Biofuel production and bioconversion
- Plant Gene Expression Analysis
- CRISPR and Genetic Engineering
- Protist diversity and phylogeny
- Bacterial Genetics and Biotechnology
- Plant Molecular Biology Research
- Transgenic Plants and Applications
- Chromosomal and Genetic Variations
- Plant biochemistry and biosynthesis
- Paleontology and Stratigraphy of Fossils
- Algal biology and biofuel production
- Insect-Plant Interactions and Control
- Marine and coastal ecosystems
- Methane Hydrates and Related Phenomena
- Plant Parasitism and Resistance
- Enzyme Catalysis and Immobilization
- Polysaccharides and Plant Cell Walls
- Metabolomics and Mass Spectrometry Studies
- Geology and Paleoclimatology Research
- Metal-Catalyzed Oxygenation Mechanisms
University of California, Berkeley
2010-2025
Joint BioEnergy Institute
2015-2024
Lawrence Berkeley National Laboratory
2015-2024
Innovative Genomics Institute
2021-2024
Joint Genome Institute
2012-2024
University of California, Davis
2018-2022
Stanford University
2018
Howard Hughes Medical Institute
2014
University of California, San Diego
2008
The cyanobacterial phylum encompasses oxygenic photosynthetic prokaryotes of a great breadth morphologies and ecologies; they play key roles in global carbon nitrogen cycles. chloroplasts all eukaryotes can trace their ancestry to cyanobacteria. Cyanobacteria also attract considerable interest as platforms for "green" biotechnology biofuels. To explore the molecular basis different phenotypes biochemical capabilities, we sequenced genomes 54 phylogenetically phenotypically diverse strains....
Inventors in the field of mechanical and electronic engineering can access multitudes components and, thanks to standardization, parts from different manufacturers be used combination with each other. The introduction BioBrick standards for assembly characterized DNA sequences was a landmark microbial engineering, shaping synthetic biology. Here, we describe standard Type IIS restriction endonuclease-mediated assembly, defining common syntax 12 fusion sites enable facile eukaryotic...
Research Article| December 08, 2017 Precise age of Bangiomorpha pubescens dates the origin eukaryotic photosynthesis Timothy M. Gibson; Gibson 1Department Earth and Planetary Sciences/GEOTOP, McGill University, Montréal, Quebec H3A 0E8, Canada Search for other works by this author on: GSW Google Scholar Patrick Shih; Shih 2Joint BioEnergy Institute, Emeryville, California 94608, USA3Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, 94720, USA Vivien Cumming;...
Abstract The rise of oxygen ca. 2.3 billion years ago (Ga) is the most distinct environmental transition in Earth history. This event was enabled by evolution oxygenic photosynthesis ancestors Cyanobacteria. However, long‐standing questions concern evolutionary timing this metabolism, with conflicting answers spanning more than one years. Recently, knowledge Cyanobacteria phylum has expanded discovery non‐photosynthetic members, including a closely related sister group termed...
The evolutionary mechanisms behind the extant distribution of photosynthesis is a point substantial contention. Hypotheses range from presence phototrophy in last universal common ancestor and massive gene loss most lineages, to later origin Cyanobacteria followed by extensive horizontal transfer into phototrophic clades, with intermediate scenarios that incorporate aspects both end-members. Here, we report draft genomes 11 Chloroflexi: Chloroflexia isolate Kouleothrix aurantiaca as well 10...
Abstract Rubisco is the primary CO 2 -fixing enzyme of biosphere 1 , yet it has slow kinetics . The roles evolution and chemical mechanism in constraining its biochemical function remain debated 3,4 Engineering efforts aimed at adjusting parameters rubisco have largely failed 5 although recent results indicate that functional potential a wider scope than previously known 6 Here we developed massively parallel assay, using an engineered Escherichia coli 7 which activity coupled to growth,...
The root knot nematode, Meloidogyne incognita, is an obligate parasite that causes significant damage to a broad range of host plants. Infection associated with secretion proteins surrounded by proliferating cells. Many parasites are known secrete effectors interfere plant innate immunity, enabling infection occur; they can also release pathogen-associated molecular patterns (PAMPs, e.g., flagellin) trigger basal immunity through the nematode stylet into cell. This leads suppression and...
Chloroplasts and mitochondria descended from bacterial ancestors, but the dating of these primary endosymbiosis events remains very uncertain, despite their importance for our understanding evolution both bacteria eukaryotes. All phylogenetic in Proterozoic before is difficult: Significant debates surround potential fossil calibration points based on interpretation Precambrian microbial record, strict molecular clock methods cannot be expected to yield accurate dates over such vast...
Abstract The antiquity and global abundance of the enzyme, RuBisCO, attests to crucial longstanding role it has played in biogeochemical cycles Earth over billions years. counterproductive oxygenase activity RuBisCO persisted years evolution, despite its competition with carboxylase necessary for carbon fixation, yet hypotheses regarding selective pressures governing evolution have been limited speculation. Here we report resurrection biochemical characterization ancestral RuBisCOs, dating...
Significance Photosynthesis supports life on our planet; however, we know very little about the origins of this metabolism. Anoxygenic photosynthesis existed prior to evolution its more complex counterpart, oxygenic photosynthesis. It is not known which groups microbes performed anoxygenic early Earth; one idea has argued that evolved in bacterial phylum Chloroflexi. We compared genomes different members Chloroflexi, finding acquisition and their unique carbon fixation metabolism remarkably...
Abstract The evolution of aerobic respiration was likely linked to the origins oxygenic Cyanobacteria. Close phylogenetic neighbors Cyanobacteria, such as Margulisbacteria (RBX-1 and ZB3), Saganbacteria (WOR-1), Melainabacteria Sericytochromatia, may constrain metabolic platform in which arose. Here, we analyze genomic sequences predict that sediment-associated have a fermentation-based metabolism featuring variety hydrogenases, streamlined nitrogenase, electron bifurcating complexes...
Abstract Human milk oligosaccharides (HMOs) are a diverse class of carbohydrates which support the health and development infants. The vast benefits HMOs have made them commercial target for microbial production; however, producing approximately 200 structurally at scale has proved difficult. Here we produce diversity by leveraging robust carbohydrate anabolism plants. This includes high-value complex HMOs, such as lacto- N -fucopentaose I. produced in transgenic plants provided strong...
Global photosynthetic productivity is limited by the enzymatic assimilation of CO2 into organic carbon compounds. Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), carboxylating enzyme Calvin-Benson cycle, poorly discriminates between and O2, leading to photorespiration loss fixed nitrogen. With advent synthetic biology, it now feasible design, synthesize, introduce biochemical pathways in vivo. We engineered a photorespiratory bypass based on 3-hydroxypropionate bi-cycle model...
Abstract The advent and growth of synthetic biology has demonstrated its potential as a promising avenue research to address many societal needs. However, plant efforts have been hampered by dearth DNA part libraries, versatile transformation vectors efficient assembly strategies. Here, we describe system (named jStack) utilizing yeast homologous recombination efficiently assemble into vectors. We demonstrate how this method can facilitate pathway engineering molecules pharmaceutical...
Significance Cellulosic biofuels have not yet reached cost parity with conventional petroleum fuels. One strategy to address this challenge is generate valuable coproducts alongside biofuels. Engineering bioenergy crops value-added bioproducts in planta can reduce input requirements relative microbial chassis and skip costly deconstruction conversion steps. Although rapid progress has been made plant metabolic engineering, there no systematic analysis devoted quantifying the impact of such...
With its ability to catabolize a wide variety of carbon sources and growing engineering toolkit,
The transcriptional effector domains of transcription factors play a key role in controlling gene expression; however, their functional nature is poorly understood, hampering our ability to explore this fundamental dimension regulatory networks. To map the trans-regulatory landscape complex eukaryote, we systematically characterized putative over 400 Arabidopsis thaliana for capacity modulate transcription. We demonstrate that activity can be integrated into networks capable elucidating...