Bacterial Genetics and Genomics

Lori A.S. Snyder

• Publisher: Garland Science
• Year: 2020
• ISBN:
  9781000039191
• Edition: 1
• Topic: Biological Sciences
• Subtopic: Genetics & Genomics
• Index: Biological Sciences

Our understanding of bacterial genetics has progressed as the genomics field has advanced. Genetics and genomics complement and influence each other; they are inseparable. Under the novel insights from genetics and genomics, once-believed borders in biology start to fade: biological knowledge of the bacterial world is being viewed under a new light and concepts are being redefined. Species are difficult to delimit and relationships within and between groups of bacteria – the whole concept of a tree of life – is hotly debated when dealing with bacteria. The DNA within bacterial cells contains a variety of features and signals that influence the diversity of the microbial world. This text assumes readers have some knowledge of genetics and microbiology but acknowledges that it can be varied. Therefore, the book includes all of the information that readers need to know in order to understand the more advanced material in the book.

Part I

DNA, Genes, and Genomes

Chapter
1

DNA

This chapter will introduce the biologically important molecule, DNA, deoxyribonucleic acid. DNA is the genetic material, carrying within its structure the code of life, thus it is important to understand how this molecule arose on Earth, how scientists determined that DNA held the code of life, what the structure of the molecule is, and how this holds the genetic information. Terms and concepts that will be explored in more detail in this book are introduced here, forming the fundamental background and concepts of bacterial genetics and genomics.

Life originated from RNA with DNA evolving later

There once was a time when there was no DNA (deoxyribonucleic acid). Billions of years in the past, before life emerged on the planet, a primordial soup of chemicals and compounds held the promise of what we have on the Earth today. In our study of genetics and genomics today, we analyze the sequence of DNA, but when investigating the distant past, it is believed that it was not DNA that was at the origin, but RNA (ribonucleic acid).

According to the RNA World hypothesis, the first nucleic acids on our planet were RNAs, which were first established as catalyst and genetic material. Early life on Earth is believed to be RNA-based, rather than DNA. Today, there exist viruses with RNA genomes that serve as examples and evidence that RNA can be the carrier of the genetic code. The discovery of ribozymes, RNA enzymes (covered in Chapter 4), has provided further supporting evidence for the RNA World hypothesis by showing that RNA can be a biological catalyst. Therefore, the necessary functions for early life on Earth can all have been accomplished by RNA in the absence of DNA. DNA-based storage of genetic information, which is seen in living cells today, came later in the evolution of life. The RNA World model, with DNA arising on Earth later, is supported by chemistry and the complexity of enzymes needed for DNA to be synthesized and therefore used as the code of life.

It is believed that DNA arose after templated protein synthesis, whereby proteins are made based on the sequence of RNA. There are some suggestions that DNA may have emerged before this process arose, although these theories still start with RNA. It is also unclear whether DNA came about before or after the Last Universal Common Ancestor (LUCA), that is, the lifeform that came before the lineage split that resulted in today’s bacteria, eukaryotes, and archaea. If DNA arose after the Last Universal Common Ancestor, this would explain fundamental key differences in the way in which errors are corrected in the genetic code between the different lineages. If, however, DNA came about before the bacteria, eukaryotes, and archaea lineages split, then the differences between the genes responsible for accurately copying DNA in bacteria versus the other lineages would have to be due to the complete replacement of these genes in the other lineages later in evolution. If DNA containing these genes and other features was present before the split, then it would follow that these genes should continue to carry similarity with one another across the three lineages. Because they do not, either DNA arose after the Last Universal Common Ancestor or it arose before and the copying accuracy genes were later swapped out for those with similarity to what is seen in the lineages today.

Over 4 billion years ago, the first life on Earth appeared. This first life form was the initial replicator, capable of making more of itself, and it was the beginning of evolution as the Initial Darwinian Ancestor (Figure 1.1). The Last Universal Common Ancestor came much later. The RNA World hypothesis would mean that Darwinian Evolution occurred in two phases: first as the RNA World of ribozymes catalyzing metabolism and RNA replication starting with the Initial Darwinian Ancestor; and then as the DNA/RNA/protein world of DNA, rRNA, mRNA, tRNA, ribosomes, and protein enzymes for metabolism, RNA synthesis, protein synthesis, and DNA replication, which continues today. Evolution, based on RNA, would have occurred before DNA arose and before the split into the prokaryote, eukaryote, and archaea lineages, in the first form(s) of life on Earth. As these progressed, evolution led to the Last Universal Common Ancestor.

Figure 1.1 Evolution of life as we know it according to the RNA World hypothesis. The world we understand now evolved from an earlier form. One hypothesis, strongly supported, is that life began as an RNA World. It is believed that 4 billion years ago, the Initial Darwinian Ancestor arose, the first life form that started evolution on Earth. From this later arose the Last Universal Common Ancestor, which diverged into the lineages we describe today as bacteria, archaea, and eukaryotes. There was a transition to the world of today, a DNA/RNA/protein world, either before or after the Last Universal Common Ancestor.

Nucleic acids are made of nucleoside bases attached to a phosphate sugar backbone

The complexity of life is determined by nucleic acids. These biological molecules are what make up DNA and RNA, the blueprints for life. All nucleic acids have two aspects: the backbone and the nucleoside bases. The nucleic acid backbone itself is made of two parts, alternating between five-carbon sugars and p...