Allies and Enemies: How the World Depends on Bacteria (18 page)

Lichen is a living entity made from a cooperative relationship between a fungus and a bacterium or an alga. Among bacteria,

cyanobacteria are by far the most common to form associations with

fungi. The photosynthesis performed by cyanobacteria helps keep the

lichen alive but also may aid the growth of other bacteria by providing organic nutrients. The limestone surfaces of the Mayan ruins at Chichen-Itza support bacteria and other microbes. The bacterial populations become denser and more diverse on the sun-bathed

stones and less dense and varied on surfaces inside temples and corridors.

Microbiologists have taken a unique tack for preventing the further deterioration of art by using other bacteria to combat the effects chapter 4 · bacteria in popular culture

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of art-degrading species. The first task involves cleaning the objects

to remove the heavy detritus that has accumulated over centuries.

Specific bacteria remove crusts of sulfates and nitrates, animal-based

glues, and the remains of molds and insects. Injecting nutrients into

the pores of art’s materials might allow bacteria to grow and form crystals that would block future infiltration of the porous surfaces.

Similar bacteria may be applied to clean the microscopic crevices of a

piece. Researcher Giancarlo Ranalli, working in Pesche, Italy, has become an expert on using bacteria to clean art. He has applied bacteria-filled poultices to clean the marble of Michelangelo’s Pieta Rondanini, and in 2007 his team reported a comparison between bacteria and a cleaning mixture of ammonium carbonate, detergent, and an abrasive applied to marble surfaces in Milan Cathedral. Desulfovibrio vulgaris cleaned the marble without removing the material’s patina while the cleaning mixture removed less dirt and left behind a precipitate. Ranalli’s team has since put Pseudomonas stutzeri to work digesting glue from protective shrouds that had covered frescoes in the Pisa Cemetery for more than 20 years. In this case, P. stutzeri’s

unique protein-degrading enzymes released the fabric without

destroying the fresco underneath.

Conservators of Europe’s galleries have been hesitant to let a microbiologist spread bacteria all over their valuable works of art.

Although bacteria like Ranalli’s have worked on stone, the same method

does not have a long track record on gallery art. Cleaning a 300-year-old painting differs from using bacteria to dissolve crud from inside restaurant grease traps, septic tanks, and wastewater holding tanks in navy ships, all current uses for Bacillus, Pseudomonas, and other bacteria.

Art-cleaning bacteria will require fine-tuning to ensure they digest unwanted dirt but leave the art’s components in good condition.

Biotechnology might help in the new field of bacteria-based art

refurbishing. Bacteria can be engineered to excrete antibiotics targeted to art-loving bacteria. Genetically modified organisms (GMOs) might also someday act on specific components in art buildup, and then stop due to a shut-off gene that activates when the target compounds are gone. In the meanwhile, bacteria gnaw on the Roman Coliseum and perhaps the Mona Lisa.

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5

An entire industry from a single cell

The biotechnology industry arrived in the late 1970s when entrepre—

neur-biologists began harnessing microbes for profit. A new company,

Genentech, first entered the commercial market in 1977 with the peptide somatostatin, made by E. coli engineered to carry genes that encoded for this growth-modulating hormone. Prior to these E. coli fermentations, somatostatin came only from cattle after slaughter.

The first success in moving genes from one organism into a different, unrelated organism occurred in 1972 in Paul Berg’s laboratory at Stanford University. Berg composed a hybrid DNA from the DNA

molecules extracted from two different viruses. The next year Her—

bert Boyer and Stanley Cohen further stretched the boundaries of gene transfer by putting genes from a toad into E. coli. Most important, successive generations of the engineered E. coli retained the new gene and reproduced it whenever they made new copies of E. coli genes. Boyer and Cohen had developed recombinant DNA, and as a result, the world had its first human-made GMO.

Some biotechnologists have taken a broad view of when their science began, citing the first use of bacteria or yeasts to benefit humans. Using this criterion, biotech began in 6000 BCE when people first brewed beverages using yeast fermentations. For practical purposes, the science of manipulating microbial, plant, and animal genes emerged when scientists first cleaved DNA and then inserted a gene from an unrelated organism into it. The biotech industry commenced when companies made the first commercial products from

recombinant DNA by growing large volumes of GMOs.

Berg, Boyer, and Cohen would not have initiated the new science

of genetic engineering without prior individual accomplishments in 99

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allies and enemies

genetics. Walther Flemming, in 1869, collected a sticky substance from

eukaryotic cells he called chromatin, later to be identified along with associated proteins as the chromosome. In most bacteria, the chromosome is a single DNA molecule packed into a dense area of the cell (called DNA packing). Bacteria do not contain the proteins, called histones, which eukaryotes use for keeping the large DNA molecule organized. Eukaryotes carry from one to several chromosomes. The eukaryotic chromosomes plus DNA located in mitochondria collectively make up the organism’s genome. In bacteria, the genome consists of the DNA plus plasmids.

In the early 1900s, Columbia University geneticist Thomas Hunt

Morgan used Drosophila fruit flies to demonstrate that the chromosome, in other words DNA, carried an organism’s genes. Less than 50

years later, American James Watson and British Francis Crick, who

were both molecular biologists, described the structure of the DNA

molecule.

DNA structure resembles a ladder that has been twisted into a helix. The long backbones, or strands, consist of the sugar deoxyribose, each holding a phosphate group (one phosphorus connected to four

oxygens) that extends away from the ladder. Deoxyribose also holds a

nitrogen-containing base on the opposite side that holds the phosphate group. Each base points inward so that different bases from each strand and complementary in structure connect by a chemical bond. These bonds, called hydrogen bonds, hold atoms together by weak connections compared with other types of chemical bonds.

Nature uses only four bases in DNA to serve as a type of alphabet.

These bases are adenine, thymine, cytosine, and guanine, which biologists abbreviate to A, T, C, and G, respectively. The sequence of bases in DNA determines the makeup of genes, which are short segments of bases. The exact sequences of A, T, C, or G in each living organism hold all of the genetic information that defines the organism’s species and also makes every individual unique. No two DNA compositions are identical.

Paul Berg and the other leading molecular biologists first created

hybrid DNA by cutting the strands with an enzyme called restriction

endonuclease. (Restriction endonucleases evolved in bacteria for

the purpose of destroying foreign DNA brought into the cell by an

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invading phage.) The break in the DNA molecule served as a place to

insert one or more genes from another organism.

An alphabet composed of only four letters does not seem adequate for carrying all the heredity of every organism on Earth. Nature

solved this potential problem by requiring that each sequence of three bases serve as the main unit of genetic information, called the genetic code. The base triplet constitutes a codon, and each codon translates to one of nature’s amino acids, which act as the building blocks of all proteins regardless of whether the proteins belong to animals, plants, or microbes. Only 20 different amino acids go into nature’s proteins that vary in length from about 100 to more than 10,000 amino acids. The three-letter codons increase nature’s capacity to put all of its information into genes made of no more than four letters. The varying lengths of proteins further expand the possibilities for defining everything in nature from a simple microbe to a human. The genetic code furthermore defines every being that once lived but has gone extinct.

Imagine if only one base were to encode for one amino acid. Pro—

teins would not be able to contain more than four amino acids. A codon

composed of two bases could hold a maximum number of amino acids

of 42,, or16. By adding one more base, the maximum number of amino

acids that the alphabet could define would be 43, equal to 64. DNA’s

triplet codons can thus identify all of the essential amino acids with

several codons to spare. Because nature tries to do things in the simplest way possible, it has no need to design four-, five-, or longer base codons to accomplish the same job performed buy a three-base codon.

Nature makes use of the extra 44 codons that do not translate directly to an amino acid by assigning some of them specific mean—

ings, such as “The gene starts here” and “The gene stops here.” The

genetic code, unlike the 26-letter alphabet used in English, contains

redundancy but no ambiguity. Redundancy allows some amino acids

to have more than one codon that defines them. For example, DNA

uses either of two codons to spell the amino acid arginine (AGA and

AGG), but six different codons can each spell the amino acid serine.

No ambiguity occurs in the genetic code, however, because no codon

ever specifies more than one amino acid. Contrast the genetic code to

the English alphabet containing the five-letter heteronym “spring,”

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allies and enemies

which could mean a mechanical device inside a mattress, a freshwater

source, the act of leaping, or a season.

Redundancy helps biological systems operate with some versatility so that even a slight mistake in a base sequence can translate into the correct amino acid used for building a protein. Cells also contain repair systems that proofread the code. Repair system enzymes excise

incorrect bases, fix mismatched bases in the ladder’s rungs, and rebuild damaged sections of DNA.

The genetic code connects all biological organisms. Regardless

of the organism from single-celled bacteria to the most complex—usually assumed by egocentric humans to be the human—all use the

same genetic alphabet to define amino acids and thus proteins. The

universal nature of the genetic code allows scientists to study E. coli for the purpose of learning about human genes. In addition, the unity of biology makes the opportunities for genetic engineering almost unlimited because every organism uses the same basic means of

building its cellular constituents.

Genetic engineering has not replaced the chemical industry,

although industry leaders in Europe have made plans to convert chemical manufacturing processes to biological processes. This new business model, called white biotechnology, uses bacteria or their enzymes to carry out manufacturing steps that presently require high heat and

hazardous catalysts. White biotech produces no hazardous waste and

requires much less energy input than conventional manufacturing.

The U.S. biotech industry familiar to most people and responsible for

making GMOs is called green biotechnology. The biotechnology

industry currently designates color codes to specific areas of interest: ·
Green
—Bioengineered microbes, food crops, and trees ·
White
—Microbial enzymes applied to industrial

manufacturing

·
Blue
—Biotechniques oriented toward marine biology

·
Orange
—Engineered yeasts

·
Red
—Medical gene therapy, tissue therapy, and stem cell

applications

In the 1950s, companies rebuilt their businesses for a peacetime

economy. The chemical industry had been expanding since the 1930s

chapter 5 · an entire industry from a single cell

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and boomed in the 1950s with a new mantra: convenience products.

DuPont Company communicated its industry’s bright future as well as

its customers’ with the slogan “Better Things for Better Living...