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Chromobacterium subtsugae genome

A technology of recombinant vector and insecticidal composition, which is applied in the direction of genetic engineering, glycosylase, recombinant DNA technology, etc., and can solve the problems of inability to restore oral toxicity of Escherichia coli

Inactive Publication Date: 2018-05-22
MARRONE BIO INNOVATIONS
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

They found that they were unable to restore oral toxicity in E. coli in the absence of the tccC-like homologue

Method used

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  • Chromobacterium subtsugae genome
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  • Chromobacterium subtsugae genome

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example

[0065] A functional approach for defining common properties of individual amino acids is to analyze the normalized frequency of amino acid changes between corresponding proteins of homologous organisms (Schulz, G.E. and R.H. Schirmer, Protein Structure Principles (Principles of Protein Structure, Springer-Verlag, 1979). From this type of analysis, it is possible to define groups of amino acids in which amino acids within a group preferentially substitute for each other in homologous proteins and thus have a similar effect on the overall protein structure (Schultz G.E. and R.H. Schimmer op. cit.) . According to this type of analysis, a "conservative amino acid substitution" refers to the substitution of one amino acid residue for another amino acid residue that shares chemical and physical properties (eg, charge, size, hydrophobicity / hydrophilicity) of the amino acid side chain. The following are examples of amino acid residues sharing certain chemical and / or physical properti...

example 1

[0264] Example 1: Cell Growth and DNA Extraction Chromobacterium hemlock PRAA-1 was grown for 24-48 hours at 26°C in 200ml of LB broth in a 1L flask rotating at 150rpm. Biomass in the culture broth was collected by centrifugation.

[0265] Genomic DNA was extracted using the MoBio Power Microbial Maxi-DNA Extraction Kit (MoBio Cat# 122223-25). DNA was eluted in 1.5 ml elution buffer (included in the kit). For analysis of DNA quality and quantity, 10 uL aliquots were loaded into a 1.5% agarose gel and electrophoresed at 100 V for 30 min. Dye was loaded using EZ-Vision and DNA was visualized with a UV transilluminator. More than 100 μg of DNA was recovered.

example 2

[0266] Example 2: DNA Sequence Determination and Assembly Using HiSeq 2000 (Illumina, San Diego, CA), sequence reads at 100 bp, pair ended, at minimum 40× coverage Rate alignment, DNA sequence determination. The final data consisted of two sets of paired-end samples in FASTQ format, providing approximately 200× genome coverage.

[0267] Assembly is performed using four FASTAQ files. FASTAQ sequences were quality-controlled using FASTQC, and the average distance between pairs was calculated by comparing the top 10,000 pairs of the two sets with the initially assembled contig using BWA. Li and Durbin (2009) Bioinformatics 25(14):1754-1760. TrimGalore (Babraham Bioinformatics, Cambridge, UK) was then used to generate two sets of high-quality paired-end sequences and four single-read files for those sequences with partner reads in Q2 After upper trimming falls below a quality threshold of at least 50 nucleotides.

[0268] Sequence reads were assembled using Ray assembler v2.0....

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Abstract

Disclosed herein is the nucleotide sequence of the Chromobacterium subtsugae genome. Also provided are the nucleotide sequences of open reading frames in the C. subtsugae genome (i.e., C. subtsugae genes). In addition, the amino acid sequences of proteins encoded by the C. subtsugae genome are provided. Nucleic acids, vectors and polypeptides comprising the aforementioned sequences are also provided. Homologues, functional fragments and conservative variants of the aforementioned sequences are also provided. Compositions having pesticidal, bioremedial and plant growth-promoting activities comprising C. subtsugae genes and proteins, and methods for the use of these compositions, are also provided.

Description

Technical field [0001] The present invention is in the field of biopesticides; specifically bacterial pesticides, their genes and their gene products. [0002] Reference to sequence listing [0003] This application contains a sequence listing that has been submitted by EFS Network in ASCII format. The name of the ASCII copy is MBI-203-0006-US-PR1_ST25.txt, and the size is 24,039,565 bytes. Background technique [0004] Chromobacterium subtsugae, a purple-pigmented bacterium (PRAA4-1), was isolated from forest soil in Maryland in 2000 (Martin et al., 2004). In an initial screen, this bacterium was found to be toxic to the Colorado potato beetle and other insect pests (Martin et al., 2007a). Further studies of the isolate revealed activity against mites, maggots, different beetle species, aphids, and plant parasitic nematodes, among other plant pests (Martin et al., 2007b; US Patent Application Publication No. 2012 / 0100236 A1). [0005] Proteases and Insect Control Prote...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12N15/63C12N15/82C07K16/12C07K16/16A01N37/18A01N63/50
CPCA01N37/46C12N9/52C07K14/42C12N9/2442C12N15/8286C12N9/24Y02A40/146A01N63/50A01N63/20C12Y302/01014
Inventor 安娜·露西娅·科尔多瓦-科雷洛斯德博拉·维尔克帕梅拉·马罗内
Owner MARRONE BIO INNOVATIONS
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