PR- genome mining

Question 1

this article is talking about what

Answer 1

mining of genome

Question 2

what is the goal of genome mining

Answer 2

to discover bioactive compounds like antibiotic, antivirus,…

Question 3

what is genome mining

Answer 3

refers to the use of experiment technique to identify genes, biosynthetic pathway and other genetic element from raw genetic data

Question 4

why do we use genome mining

Answer 4

• used to identify biosynthetic gene cluster encoding the organisms
• used to identify biosynthetic gene clusters encoding/synthesizing compounds containing specific characteristic/properties
  -this method is used to explore the microbial genome for discovery of secondary metabolite
• it can also reveal new biochemical insight of the organism
• make it possible to know the gene that encode Non-ribosomally synthesized peptides (NRPs) in bacteria
• currently, is being used in identification of core biosynthetic enzyme in genomic data which can be a valuable target from identifying new biosynthetic gene cluster

Question 5

what are Different Genome Mining Techniques:

Answer 5

1. Single Cell Genome Mining: allow the analysis of individual cells
2. metagenome mining: involved studying of genetic material recovered directly from the environmental sample.
   3.Regulation-based Genome Mining: focus on finding the gene cluster that generated under the specific condition.
3. Resistance-based Genome Mining: target gene cluster that associate with antibiotic, so it help to discovery gene that combat the resistance.
   5.Phylogeny-based Genome Mining: identification of gene cluster based on the evolution.
   6.Comparative Genome Mining: compare genome from different species
   7.Classical Genome Mining: used to identify gene cluster

Question 6

what is Reverse Genetics and Heterologous Expression

Answer 6

Reverse Genetics: identifying gene based on their function
Heterologous Expression: this method allow the express of gene from one organism in another to study the gene product like second metabolites

Question 7

what instrument can we use manual to identify mining of gene encoding biosynthetic enzyme

Answer 7

BLAST

Question 8

use of antiSMASH

Answer 8

identify different gene cluster type

Question 9

what does the genome mining lead to

Answer 9

identification of the bioactive metabolite

Question 10

where did classical genome mining used

Answer 10

used for the research of the enzyme used in the biosynthesis of the secondary metabolite like:

1. genes encoding core-biosynthetic enzymes
2. genes encoding Polyketides
3. genes encoding Non-ribosomally synthesized peptides (NRPs)
4. gene encoding ribosomally synthesized and post-translationally modied peptides (RiPPs): Researchers used bioinformatics tools like PSI-BLAST to mine microbial genomes for homologues of the LanM enzyme, leading to the discovery of new strains capable of producing lanthipeptides.
5. Terpenoids/isoprenoids
   6 Screening for tailoring enzymes

Question 11

where and how did Comparative genome mining be used

Answer 11

when we want to identify and analyze the biosynthetic gene cluster across different microbial genome/organism

it was used by comparing genetic sequence and structures among various organism and we can be able to identify the similarities and difference that can indicate the presence or absence of the novel compounds.

it involve in the search of the gene that encode the enzymes responsible for the biosynthesis of secondary. metabolite

Question 12

what can we use to have success Comparative genome mining

Answer 12

we can use antiSMASH that allow us to compare identified BGCs with the large data base known GBCs

Question 13

where and how did Phylogeny based mining methods be used

Answer 13

utilize the evolutionary relationship among the organism to guide discovery and analysis of the BGCs responsible for producing secondary metabolite