Ginkgo Bioworks, Inc.

Iti Scotland Limited

Reshma P Shetty

Curt R Fischer

Austin J Che

Jason R Kelly

Thomas F Knight, Jr

Randall David Rettberg

Jason Kelly

Austin Che

Tom Knight

Barry Canton

Maiwenn Kersaudy Kerhoas

Farid Amalou

Will Shu

Kersaudy Kerhoas Maiwenn,

Patrick Boyle

The present disclosure identifies pathways, mechanisms, systems and methods to confer chemoautotrophic production of carbon-based products of interest, such as sugars, alcohols, chemicals, amino acids, polymers, fatty acids and their derivatives, hydrocarbons, isoprenoids, and intermediates thereof, in organisms such that these organisms efficiently convert inorganic carbon to organic carbon-based products of interest using inorganic energy, such as formate, and in particular the use of organisms for the commercial production of various carbon-based products of interest.

Chemoautotrophic cells comprising an engineered carbon fixation pathway

The present disclosure identifies pathways, mechanisms, systems and methods to confer production of carbon-based products of interest, such as sugars, alcohols, chemicals, amino acids, polymers, fatty acids and their derivatives, hydrocarbons, isoprenoids, and intermediates thereof, in engineered and/or evolved methylotrophs such that these organisms efficiently convert C1 compounds, such as formate, formic acid, formaldehyde or methanol, to organic carbon-based products of interest, and in particular the use of organisms for the commercial production of various carbon-based products of interest.

Methods and systems for methylotrophic production of organic compounds

Methods for making chemoautotrophic cells by engineering an energy conversion pathway and a carbon fixation pathway

Systems, methods, libraries, kits, and computer software tools are provided for designing and producing engineered cells. Such engineered cells can be used for cell state quantification, such as genome, transcriptome and/or proteome quantification. In one aspect, an engineered cell having a plurality of artificially designed oligonucleotides introduced into the genome of the cell is provided. The oligonucleotides are each located in proximity of a gene of interest encoding a protein of interest, and are different from one another. The oligonucleotides can each encode a unique peptide tag for each protein of interest, wherein each peptide tag has a unique quantitatively measurable value such as mass-to-charge ratio which can be quantified by a mass spectrometer. The engineered cell is capable of expressing a plurality of proteins of interest each fused to its corresponding unique peptide tag, wherein each peptide tag is capable of being released therefrom.

Methods and systems for cell state quantification

Methods and systems for chemoautotrophic production of organic compounds

Provided herein are methods for the assembly of a polynucleic acid sequence that is at least partially carried out on a microfluidic device; methods for the preparation of a library of polynucleic acid sequences; microfluidic devices; methods for designing nucleic acid sequences; methods for planning the assembly of a polynucleic acid sequence from a plurality of nucleic acid sequences; systems comprising components for carrying out these methods; computer programs which, when run on a computer, implements these methods; and computer readable medium or carrier signals encoding such a computer program.

Method for the assembly of a polynucleic acid sequence

The present invention provides a method for the assembly of a polynucleic acid sequence from a plurality of nucleic acid sequences in which the polynucleic acid sequence is of a formula N, in which N represents a nucleic acid sequence and where n is 1 or greater than 1 and each N may be the same or a different nucleic acid sequence, in which the method comprises: (i) providing a first nucleic acid sequence N1 which has an oligonucleotide linker sequence L1at the 3'-end of the nucleic acid sequence; (ii) providing a second nucleic acid sequence N2 which optionally has an oligonucleotide linker sequence L2at the 3&#x2032;-end of the nucleic acid sequence and which has an oligonucleotide linker sequence L2at the 5&#x2032;-end of the nucleic acid sequence, wherein the 5&#x2032;-end linker sequence L2of nucleic acid sequence N2 is complementary to the 3&#x2032;-end linker sequence L1of nucleic acid sequence N1; (iii) optionally providing one or more additional nucleic acid sequences N, wherein nucleic acid sequence N2 has an oligonucleotide linker sequence L2at the 3&#x2032;-end of the nucleic acid sequence, and wherein said one or more additional nucleic acid sequences N comprises a terminal additional nucleic acid sequence NZ, and wherein each additional nucleic acid sequence N has an oligonucleotide linker sequence at its 3&#x2032;-end, wherein said terminal additional nucleic acid sequence NZ optionally lacks an oligonucleotide linker sequence at its 3&#x2032;-end and wherein each additional nucleic acid sequence N has an oligonucleotide linker sequence at its 5&#x2032;-end, wherein for the first additional nucleic acid sequence N3 the 5&#x2032;-end linker sequence L3is complementary to the 3&#x2032;-end linker sequence L2of nucleic acid sequence N2 and for each second and subsequent additional nucleic acid sequence N the 5&#x2032;-end linker sequence is complementary to the 3&#x2032;-end linker sequence of the respective preceding additional nucleic acid sequence; and (iv) ligating said nucleic acid sequences to form said polynucleic acid sequence.

Method for assembly of polynucleic acid sequences

Growing community of inventors

Boston, MA, United States of America

Reshma P Shetty