The Language of Life How Cells Communicate in Health and Disease (2005) / Chapter Skim
Currently Skimming:

1 Small Talk
Pages 9-40

The Chapter Skim interface presents what we've algorithmically identified as the most significant single chunk of text within every page in the chapter.
Select key terms on the right to highlight them within pages of the chapter.


From page 9...
... If you are the bacterium Escherichia coli, sharing space in the human gut with other indigenous flora and fauna, this is your world: unpredictable, at times even inhospitable. But don't dwell on your limitations.
From page 10...
... Should an appetizing snack appear on the horizon, the rotor lingers in counterclockwise mode, so that you swim straight ahead, in the direction of the meal, instead of meandering aimlessly. A distasteful substance, on the other hand, shifts the rotor clockwise, and you tumble in search of an escape route -- the path you'll follow when it resumes its usual alternating pattern.
From page 11...
... coli detect a chemical signal, however, the information will be relayed to the motor turning the flagella, causing the flagella to rotate preferentially in one direction.
From page 12...
... Nothing that might upset the delicate balance critical to life can penetrate this barrier -- but neither can the chemical signals bearing news about current events. Inside your hermetically sealed bubble, the rotor proteins controlling your flagella are waiting for direction; outside, messengers with the information needed by the rotor proteins mill restlessly in front of closed doors.
From page 13...
... Scores of fragile alliances between amino acids act in concert to stabilize the folded protein, resulting in a three-dimensional configuration as unique as a fingerprint. Productive only when wedded to another molecule, the protein relies on this structure to play the role of matchmaker, embedding an advertisement for a soul mate in the loops, bulges, and trenches created on its outer surface by the folds: "Are You My Better Half?
From page 14...
... The receptor that biologists call "Tsr" is married to the amino acid serine. The Tar receptor's partner is aspartate.
From page 15...
... ; phosphorylated CheY (5) , in turn, tells the rotor protein, currently turning counterclockwise (6)
From page 16...
... , CheA, like its kin, responds to a wake-up call with an expletive -- "Phosphate! " The chemical group that puts the "P" in ATP, phosphate, bristling with three negative charges, has the power to twist proteins inside out, turn ordinary amino acids into powerful magnets, and disrupt longstanding relationships -- a switch flipping switches.
From page 17...
... "You can think of chemotaxis receptors as sitting in a balance between the ligand binding state and the methylation state (that is, the number of methyl groups attached to the receptor protein) ," explains Ann Stock.
From page 18...
... coli illustrates fundamental principles common to the transfer of any type of biological information via chemical signals: the exploitation of protein topography to discriminate signals; the use of transmembrane receptors to circumvent the barrier posed by the plasma membrane; the coordination of perception and response, as well as the integration of multiple signals, by means of protein relays featuring kinases; the regulation of receptor sensitivity by chemical modification. Using these principles as a template, evolution would construct a chemical language that would end the isolation of cells, that would allow them to talk to one another, to cooperate, to live as a group yet behave as a single organism -- one of the most extraordinary achievements in the history of life.
From page 19...
... I poke more aggressively. Without warning the stalks supporting the crabs' beady black eyes shoot straight up at me.
From page 20...
... Instead of transferring the microbes to petri dishes, however, they corralled them in small diffusion chambers formed by sealing a washer between two permeable membranes, placed them back on their native sand in a marine aquarium, and submerged the chambers in seawater, in effect "returning" the bacteria to the wild. Cultured the traditional way, less than 1 percent of the bacteria originally isolated would have survived; surrounded by the comforts of home, 22 percent, including two previously unknown species, not only survived but thrived.
From page 21...
... It's a win-win proposition for everyone: the plant finds a mate; the bee feeds its brood. In the moonlit shallows off the coast of a South Sea island, the Hawaiian bobtail squid Euprymna scolopes and the marine bacterium Vibrio fischeri have negotiated an equally beneficial arrangement.
From page 22...
... fischeri produces an enzyme, luciferase, facilitating a chemical reaction that releases energy in the form of light. The luminescent bacteria ensconced in the light organ enjoy a free meal, while the illuminated squid avoids becoming someone else's.
From page 23...
... "If the bacteria wait, and they count themselves, and then they all do it together, they can have an enormous impact and frankly overcome tremendous odds," she continues. Known to microbiologists as "quorum sensing," this show of hands allows the group to "organize [itself]
From page 24...
... . Within the confines of the squid light organ, however, the concentration of acyl HSL increases as the number of bacteria increases (B)
From page 25...
... Communication by quorum sensing helps the bacteria time the release of their virulence factors to coincide with a critical population density, evading detection until the cohort is large enough to take on the defenders and win. Gram-positive bacteria, such as the common soil microbe Bacillus subtilis, also count heads.
From page 26...
... B subtilis and other Grampositive bacteria have their own way of saying things, in oligopeptides, short chains of amino acids cut from larger proteins and shipped out of the transmitting cell on the back of a dedicated transport protein.
From page 27...
... As a result, they argue, quorum sensing is not simply a bacterial idiosyncrasy but "one of the first steps in the development of multicellular organisms." THE TALK OF THE TOWN "Now the whole earth had one language and few words." According to the biblical account of the Tower of Babel, the human race wouldnt' need translators if it werent' for a few arrogant architects-wed all still be speaking the same language. Instead, a bewildering ' array of at least 6,000 different tongues and regional dialects confounds international communication, impedes commerce, and undermines diplomacy.
From page 28...
... So he handed me a little vial of marine bacteria and told me to figure out how they stick," she recalls. Afterward, when she wanted to master the tools and techniques of the DNA trade, the incandescent talents of marine Vibrio species again made them the perfect lab partners.
From page 29...
... To their surprise, the search uncovered a nearly identical gene in more than 40 other species of bacteria, Gram-positive as well as Gram-negative, including a "list of the clinical `Whos' Who' in pathogenesis": Vibrio cholerae, the cholera-causing black sheep of the Vibrio family; several Salmonella and Streptococcus species; the respiratory pathogen Haemophilus influenzae; Borrelia burgdorferi, responsible for Lyme disease; Helicobacter pylori, maker of ulcers; and Yersinia pestis, infamous as the causative agent in bubonic plague. "As far as we can tell," says Bassler, "they're all making the identical molecule.
From page 30...
... "We wondered, `Couldnt' we take the receptor to go into this mix and pick out the right structure? ' So my colleague and friend Fred Hughson crystallized the sensor protein bound to the true autoinducer.
From page 31...
... A rock, a pipe, your teeth, plastic or glass, even the interface between a container of water and the overlying air, are potential building sites -- provided they're up to standard, because bacteria are as choosy about the neighborhood as any other potential homeowner. For some species a feast of sugars, or the perfect blend of amino acids, is the selling point, as compelling as an ocean view or award-winning schools.
From page 32...
... "The matrix keeps them from swimming away." If a warm rock is a homestead, a warm rock dotted with such "microcolonies" is prime real estate. Families expand their territory, newcomers crowd in, late arrivals snatch the last parcels of open space.
From page 33...
... These canals -- in reality, fluid-filled channels dredged by growth-inhibiting secretions oozing from the bacteria themselves-form a primitive circulatory sytem, piping nutrients to those living in the high-rises and draining away dissolved waste products. Cultural diversity and economic inequality, as characteristic of bacterial cities as our own, give rise to a patchwork of ethnic neighborhoods reflecting the uneven distribution of resources, regional differences in gene expression, and a willingness to accommodate multiple species.
From page 34...
... Enzymes blowtorch holes in the web of glycoproteins, pillars and mushrooms collapse, channels dilate and then disappear, as clumps of bacteria pull free and swim away in search of greener pastures. Dont' think of this breakdown as a disaster -- deconstruction is part of the natural life cycle of bacterial cities.
From page 35...
... Through the artful use of tribal dialects and a chemical lingua franca, bacteria can transcend their humble origins and mimic the great civilizations of larger organisms. A PATTERN LANGUAGE In his books, The Timeless Way of Building and A Pattern Language, architect Christopher Alexander describes a "vocabulary" of design elements he believes are essential to the construction of towns, neighborhoods, and buildings in harmony with their surroundings, because they are "deeply rooted in the nature of things." The words in this language are descriptions that Alexander calls patterns, configurations of architectural features that bear a particular relationship to one another: In a gothic cathedral, the nave is flanked by aisles which run parallel to it.
From page 36...
... Chemical signals, and the machinery that cells evolved to detect and interpret them, became lifes' parts of speech; the conventions observed when these elements were grouped to form pathways, the rules of biological syntax; the sequences constructed according to these rules, grammatically correct statements capable of informing behavior. This language, based on molecules rather than sounds -- particularly proteins, folded, coiled, and looped into "configurations of architectural features that bear a particular relationship to each other" -- has a three-dimensional aspect missing from spoken language.
From page 37...
... Receptor proteins, with a sensor component to recognize the signal, a lipid-loving segment to insinuate it in the membrane, and a cytoplasmic component to broadcast the news of signal binding inside the cell solved the problem of ferrying information across an impenetrable barrier. Problem: Delivering the mail.
From page 38...
... These conversations, an extension of sensory mechanisms developed to coordinate responses to environmental stimuli, allow them to socialize as our cells do, to build communities with many similarities
From page 39...
... SMALL TALK 39 to complex differentiated tissues, and, in so doing, to enjoy improvements in the quality of life -- better nutrition, more stability, safety from predators -- that are the perquisites of multicellular living. By exploiting the distinctive architecture of proteins and their affinity for a select group of signaling molecules, bacteria have crafted a language, talked their way to becoming the longest-running life forms on earth, and set the stage for more ambitious adventures in multicellularity.


This material may be derived from roughly machine-read images, and so is provided only to facilitate research.
More information on Chapter Skim is available.