What is Bacterial Genomics?

The study of the morphological, physiological, and evolutionary aspects of the bacterial genome is referred to as bacterial genomics. This subdisciplinary field aids in understanding how genes are assembled into genomes. Further, bacterial or microbial genomics has helped researchers in understanding the pathogenicity of bacteria and other microbes.

What is the structure and diversity of microbial genomes?

The analysis and comparison of the microbial genome with the genome of other organisms of the same or other domains are carried out at several levels. These levels comprise analyzing the guanine and cytosine content, gene organization, presence of transposons, overall size, etc. When genome sequencing was not known, information regarding the structure of microbial genome was fairly limited. At that time, pulsed-field gel electrophoresis and physical mapping (by cleaving the genome sequences with restriction enzyme) were the two techniques used to study the structure of the microbial genome. The information obtained through these techniques explained the contrast between archaeal and bacterial genomes.

Size of chromosomes

Among the sequenced bacterial genomes, the chromosome size ranges from 580 kbp (of Mycoplasma genitalium) to 9105 kbp (of Bradyrhizobium japonicum). The size of almost 90% of the sequenced bacterial genomes is less than 5.5 Mbp. Due to variations in morphological characteristics, metabolism and several other factors, different bacteria have different genomic sizes. For the bacterial species Bacillus anthracis, Bacillus cereus, Escherichia coli, Mycobacterium tuberculosis, Prochorococus marinus, Salmonella enterica Typhi, Shigella flexneri, Staphylococcus aureus, Streptococcus pyogenes, Vibrio vulnificus, and Yersinia pestis, several strains have been sequenced till now.

Different strains of bacterial species have similar genomic sizes, except E. coli and P. marinus. The E. coli strain K12-MG1655 has a genomic size of 4.6 Mbp, whereas the largest E. coli serotype, O157:H7, has a genomic size of 5.6 Mbp.

In contrast to bacterial species, the genomes of only a few archaeal species have been sequenced. Further, the difference in the size of the genome of archaeal species is not as vast as that of bacterial species. The size of the genomic content ranges between 0.5 to 5.8 Mbp for all archaeal species sequenced to date.

Chromosome number and topology

Most bacterial genomes are double-stranded circular DNA (deoxyribonucleic acid), while certain species bear linear DNA. Borrelia burgdorferi was the first bacterial species discovered with linear DNA. Apart from B. burgdorferi, several Streptomyces species also possess linear chromosomes.

Genome sequencing showed that the genomes of spirochete species Leptospira interrogans, Borrelia burgdorferi and Treponema pallidum are quite diversified. Leptospira interrogans bear a large circular chromosome of 4.33 Mb and a small circular chromosome of 359 kb. T. pallidum bears a circular chromosome of 1138 kb, and B. burgdorferi bears a linear chromosome of 911 kb.

The genome sequencing of three Vibrio species, V. cholerae, V. vulnificus, and V. parahaemolyticus, showed the presence of two circular chromosomes. Through pulsed-field gel electrophoresis, it was observed that the genome of Burkholderia cepacia (a soil-borne respiratory pathogen that affects patients with cystic fibrosis) contains multiple circular chromosomes. The overall size of the genome of the pathogen ranges from 5 to 9 Mb. A Gram-positive bacterial species, Deinococcus radiodurans, bears two circular chromosomes of 2.65 Mb and 0.412 Mb and a megaplasmid of 0.178 Mb. The bacterium is known for its extreme resistance to radiation and oxidative stress, partly due to its polyploid genome and certain DNA repair genes.

Variation in molar G/C content

The guanine and cytosine content in the genome of bacterial species can range from 24.9% (in Mycoplasma mobile) to 74% (in Micrococcus luteus). The G+C content in the genome of the members of the same species is similar (less than 1% deviation). The G+C content of the genome of closely related bacterial species and certain distantly related bacterial species is also similar.

Codon usage diversity among microbes

In 1961, Crick, Barnett, Brenner, and Watts-Tobin demonstrated that three bases code for a single amino acid. Later, the genetic code was established. The genetic code is the set of rules used by living cells for translating genetic information encoded by RNA (ribonucleic acid) or DNA into proteins. This code consists of codons that are triplets of nucleotides and code for specific amino acids. The genetic code is universal as it is identical in several organisms, including the tobacco mosaic virus, humans, E. coli, and bacteriophages. Universally, there are 64 triplet bases or codons, out of which 61 codons code for 20 amino acids (degenerate nature of the genetic code). The remaining three codons are referred to as stop codons.

In 1981, the first deviation in the standardized genetic code was observed when it was discovered that in the mammalian mitochondria DNA, AUA codon encodes for methionine instead of isoleucine, and UGA encodes for tryptophan instead of acting as a stop codon. It was also found that in Mycoplasma capricolum, CGG does not code for any amino acid.

Mutations

Mutations refer to the beneficial or deleterious alterations in the genomic sequence of an organism, a sequence of extrachromosomal DNA, or a virus. Mutations generally occur due to exposure to mutagens, DNA replication errors, or viral infections.

The mutations in codons that do not change any amino acid in a polypeptide sequence are called synonymous mutations. They are also called silent mutations because they do not change the protein structure. The mutations in codons that change any amino acid in a polypeptide sequence are called nonsynonymous mutations. They change the entire polypeptide sequence and thus the protein structure.

The mutation rate allows changes in one or more copies of alleles that pass to the next generation. It helps in determining the spontaneity of mutations occurring in a population of organisms. Nonsense mutations are the mutations that generate the stop codon. The generated stop codon terminates the translation process. The protein structure does not complete because no more amino acids can be added to the growing peptide chain.

Inserting or deleting a single nucleotide in a codon can shift the reading frame and thus change the encoding amino acids. This can inactivate the protein and cause malfunctioning. The deletion of three nucleotides from the gene results in no coding for that amino acid and its elimination from the polypeptide sequence. This may or may not alter protein functioning.

The mutation rates are higher for nonsynonymous substitutions in the regions where the genes affect the least functions. Changes in the third position of the codon, introns, and flanking regions are associated with higher rates of nonsynonymous substitutions. The rate of synonymous mutations is low as they do not affect the functioning of the gene. The mutation rates for nonsynonymous mutations are also low. It is so because high rates of nonsynonymous mutations negatively impact gene expression.

Horizontal gene transfer

In bacteria, horizontal gene transfer involves the transfer of genetic material from one bacteria species to another. The recipient, in this case, is not the offspring of the donor. This process allows a bacterium to respond to changing environments and rapidly adapt to them.

Bacterial conjugation

Bacterial conjugation involves the transfer of genetic material between two bacteria through direct contact. The F plus (donor) cell, containing the F plasmid, directly connects to the F minus (recipient) cell and forms a conjugation tube. The F plasmid opens at the origin of replication (Ori), where one strand gets cleaved, and the 5'-end of the plasmid DNA enters the recipient cell through the conjugation tube. Both the recipient and donor cells possess a single strand of the F- plasmid. This is followed by the synthesis of a complementary strand by both cells. Thus, the recipient cell also possesses a copy of the F-plasmid and becomes a viable donor cell.

Bacterial transduction

Bacterial transduction is the process of gene transfer from one cell to another through a bacteriophage. In general transduction, the bacteriophage first targets the donor cells and starts the lytic cycle. The virus forms its components with the help of the host cell machinery. The host cell DNA is then split into smaller pieces by the viral enzymes. In special transduction, limited genes are transferred into the recipient bacteria through the donor bacteria. It is performed by a temperate bacteriophage that undergoes the lysogenic cycle. The virus enters the bacterium and releases its genome inside the host cell. It remains inactive and transfers from generation to generation. The lytic cycle starts when the lysogenic cell interacts with some external stimulus. The viral genome incorporates with the genome of the host cell and transfers it to the recipient cell, where both genomes combine.

Bacterial transformation

Students often assume that all bacterial species possess the same genes, which is not true. Bacterial species differ in their genetic content, but they also share similarities that make them close relatives.

Common Mistakes

Students often assume that all bacterial species possess the same genes, which is not true. Bacterial species differ in their genetic content, but they also share similarities that make them close relatives.

Context and Applications

This topic is significant for the professional exams of undergraduate, graduate, and postgraduate courses, especially:

• Bachelor of Science in Microbiology
• Master of Science in Microbiology
• Doctor of Philosophy in Microbiology
• Master of Philosophy in Microbiology

Related Concepts

• Molecular Biology
• Molecular Genomics
• Microbial Genomics
• Bacteria Genome

Practice Problems

Q1: What is meant by the degeneracy of the genetic code?

(a) One or more codons encode a specific amino acid

(b) One codon encodes a specific amino acid

(c) No codon encodes a specific amino acid

(d) Two different codons encode different amino acids

Correct option: (a)

Q2: Which codon in Mycoplasma capricolum does not code for any amino acid?

(a) CGG

(b) AUG

(c) AGU

(d) UUU

Correct option: (a)

Q3: Which mutation in codons does not change an amino acid in a given polypeptide chain?

(a) Nonsynonymous mutation

(b) Quick mutation

(c) Slow mutation

(d) Synonymous mutation

Correct option: (d)

Q4: Which mutation in codons can change any amino acid in a given polypeptide chain?

(a) Nonsynonymous mutation

(b) Quick mutation

(c) Slow mutation

(d) Synonymous mutation

Correct option: (a)

Q5: What is the possibility of changes in one or more copies of alleles that pass over to the next generation called?

(a) Generation time

(b) Mutation rate

(c) Radioactive rate

(d) Decomposition rate

Correct option: (b)