Microbial Functional Genomics Chapter 1 Genomics Toward A

Microbial Functional Genomics Chapter 1. Genomics: Toward A Genome-Level Understanding of the Structure, Functions, and Evolution of Biological Systems CBBL - Young-sik Sohn-

Introduction � Understanding the physiology and behavior of an organism Determination of an entire genome sequence ↓ Elucidate the functions of these sequences ↓ Providing meaning to the nucleotide sequence data

Bioinformatics/Functional Genomics

Definitions and Classification � Genomics � described a new scientific discipline concerned with mapping, sequencing, and analyzing genomes � genome-level understanding of the molecular basis of the structure and functions � using whole-genome sequence information and highthroughput genomic technologies

Concept and classification of genomics

Challenges of Studying Functional Genomics � Defining gene function � Substantial portions of ORFs are functionally unknown � Relationships of genes to enzymes are not only one to one � Identifying and characterizing the molecular machines of life � Many protein machines appear to be highly conserved � Delineating gene regulatory networks � Coordinated behavior of genetic regulatory networks determines the physiological properties of a living cell

Challenges of Studying Functional Genomics � System-level understanding of biological systems beyond individual cells � Relationship between biodiversity and functional properties of ecosystems is important � Computational challenges � Using computer model to know biological cellular functions � Multidisciplinary collaborations � Collaborations among investigators with different research capabilities are needed to meet these challenges

Scope and General Approaches � Structural genomics function of a protein ≈ three-dimensional structure ∴ understanding folded structure ↓ biochemical functions or role in a pathway

Scope and General Approaches � Transcriptomics � Comprehensive analysis of transciptomes is of great value for studying gene function and regulation ① correlation of gene expression and function ② connection between gene expression and physiological states ③ gene expressed together may function together ④ importance of transcriptonal regulation ⑤ technological advances

Scope and General Approaches � Proteomics � It can be classified into three main categories ① protein identification and analysis ② proteome-wide differential display of proteins under various growth conditions ③ protein-protein interactions

Scope and General Approaches � Metabolomics � Two major approaches to understand gene functionality via metabolic analysis ① identify the biochemical reactions catalyzed by enzymes encoded by genes of unknown function ② functional analysis by coresponses

Importance of Microbial Functional Genomics to the Study of Eukaryotes � Functional analysis of microbial genomes Crucial to understanding gene functions and regulatory networks in microorganisms themselves ↓ Defining networks in higher organisms ∵ ① many genes involved in essential life processes are conserved among microorganisms ② Mitochondria and chloroplasts are important components of eukaryotic life processes ③ Many microorganisms have formed intimate relationships with higher eukaryotes

Summary � The goal is to use genome sequence information and related genomic technologies to link sequences with functions and phenotypes and to understand how biological systems at different levels function in nature � Microbial genome is not only important to understanding microorganisms themselves but also very important to higher organisms

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