Microbiology and Immunology

WORLD OF MICROBIOLOGY AND IMMUNOLOGY Proteomics

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topoisomerase III does the proofreading of the transcribed

sequences, eliminating those containing errors. Ribonuclease H

removes RNAsequences from polymers containing complexed

RNA/DNA, and DNA-ligase unites the newly transcribed frag-

ments, thus forming the new DNA strand.

In the last decade, researchers discovered that many

proteins involved in intracellular communication are struc-

tured in a modular way. In other words, they are constituted by

relatively short amino acid sequences of about 100 amino

acids, and have the basic role of connecting one protein to

another. Some proteins of such signaling pathways are entirely

comprised of connecting modules and deprived of enzymatic

activity. These non-enzymatic modules are termed protein

dominium or protein modules, and they help enzymes in the

transmission of signals to the cell nucleusin an orderly and

controlled way. Proteins containing only connecting (or bind-

ing) modules, such as SH2 and SH3, act as important molecu-

lar adaptors to other proteins. While one of its modules binds

to a signaling complex, such as a transmembrane tyrosine-

kinase receptor, other binding modules permit the docking of

other proteins that, once complexed, amplifies the signal to the

nucleus. Such adaptor proteins also allow the cell to utilize

certain enzymes that otherwise would not be activated in a

given signaling pathway. The structure of adaptor proteins

also displays binding sites that connect to DNA, where they

recognize specific nucleotide sequences of a given gene, thus

inducing transcription. In this case, the only enzyme in the

cascade of signals to the nucleus is the receptor in the surface

of the cell, and all the events that follow occur through the

recognition among proteins and through the protein recogni-

tion of a locus in DNA.

Proteins are encoded by genes. A gene usually encodes

a nucleotide sequence that can be first transcribed in pre-mes-

senger RNA, and then read and translated on the ribosomes

into a group of similar proteins with different lengths and

functions, known as protein isoforms. A single polypeptide

may be translated and then cut by enzymes into different pro-

teins of variable lengths and molecular weights.

During transcription, the non-coding DNA sequences

(introns) are cut off, and the coding sequences (exons) are

transcribed into pre-messenger RNA, which in turn is spliced

to a continuous stretch of exons before protein translation

begins. The spliced stretch subdivides in codons, where any

of the four kinds of nucleotide may occupy one or more of

the three positions, and each triplet codes for one specific

amino acid. The sequence of codons is read on the ribo-

somes, three nucleotides at a time. The order of codons

determine the sequence of amino acids in the protein mole-

cule that is formed.

Introns may have a regulatory role of either the splicing

or the translational process, and may even serve as exons to

other genes. After translation, proteins may also undergo bio-

chemical changes, a process known as post-translation pro-

cessing. They may be either cut by enzymes or receive special

bonds, such as disulfide bridges, in order to fold into a func-

tional structure.

See alsoBiochemistry; Cell cycle (eukaryotic), genetic regu-

lation of; Cell cycle (prokaryotic), genetic regulation of; DNA

(Deoxyribonucleic acid); Transcription; Translation

PProteomicsROTEOMICS

Proteomics is a discipline of microbiology and molecular biol-

ogythat has arisen from the genesequencing efforts that cul-

minated in the sequencing of the human genome in the last

years of the twentieth century. In addition to the human

genome, sequences of disease-causing bacteria are being

deduced. Although fundamental, knowledge of the sequence

of nucleotides that comprise deoxyribonucleic acidreveals

only a portion of the protein structure encoded by the DNA.

Because proteins are an essential element of bacterial structure

and function (e.g., role in causing infection), the knowledge of

the three-dimensional structure and associations of proteins is

vital. Proteomics is an approach to unravel the structure and

function of proteins.

The word proteomics is derived from PROTEin com-

plementto a genOME. Essentially, this is the spectrum of pro-

teins that are produced from the template of an organism’s

genetic material under a given set of conditions. Proteomics

compares the protein profiles of proteomes under different

conditions in order to unravel biological processes.

The origin of proteomics dates back to the identification

of the double-stranded structure of DNA by Watson and Crick

in 1953. More recently, the development of the techniques of

protein sequencing and gel electrophoresisin the 1960s and

1970s provided the technical means to probe protein structure.

In 1986, the first protein sequence database was created

(SWISS-PROT, located at the University of Geneva). By the

mid-1990s, the concept of the proteome and the discipline of

proteomics were well established. The power of proteomics

was manifest in March 2000, when the complete proteome of

a whole organism was published, that of the bacterium

Mycoplasma genitalium

Proteomics research often involves the comparison of

the proteins produced by a bacterium (example, Escherichia

coli) grown at different temperatures, or in the presence of dif-

ferent food sources, or a population grown in the lab versus a

population recovered from an infection. Escherichia coli

responds to changing environments by altering the proteins it

produces. However, the full extent of the various alterations

and their molecular bases are largely unknown. Proteomics

research essentially attempts to provide a molecular explana-

tion for bacterial behavior.

Proteomics can be widely applied to research of diverse

microbes. For example, the yeastSaccharomyces cerevisiae

is being studied to reveal the proteins produced and their func-

tional associations with one another.

The task of sorting out all the proteins that can be pro-

duced by a bacterium or yeast cell is formidable. Targeting of

the research effort is essential. For example, the comparison of

the protein profile of a bacterium obtained directly from an

infection (in vivo) with populations of the same microbe

grown under defined conditions in the lab (in vitro) could

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