Small Things Considered

Smallest Things Considered

by Merry

Oddly, coconut palms have
only one known bacterial
disease, one possible viral
disease, but at least two
diseases caused by viroids.
The tree in the foreground
is infected with cadang-
cadang, a viroid disease,
and shows symptoms of yel-
lowing, stunting, and lack
of fruit production. Source.

What do stunted coconut palms, misshapen potato tubers, and peach trees with necrotic branches have in common? They are three of the numerous crops stricken with diseases caused by viroids, an astonishing group of minimalist plant pathogens. There isn't much to a viroid, just one single-stranded, circular RNA molecule. The largest viroid genome so far is 399 nucleotides, the smallest a mere 246—about one tenth the size of the smallest viruses (hepadnavirus) and one hundredth the size of more typical viruses. Being labeled as "subviral," they are even less likely than the viruses to be granted a place on the tree of life. They get by without capsid or membrane shell. They encode no proteins. They don't reverse-transcribe into DNA when they replicate. They never insert into the host genome. Some of them cause disease symptoms, some don't. They simply replicate inside plant cells and then their progeny move on to the next location to repeat the process. Their very existence raises questions, many without answers.

What does a viroid look like? Well, that depends on the viroid. The thirty-plus species known so far fall into two groups. Most belong to the Pospiviroidae (PSTVd), named after the Potato Spindle Tuber ViroiD. Four species, including the Avocado SunBlotch ViroiD, make up their own group, the Avsunviroidae (ASBVd). Although all of them lack protective capsids, they are nevertheless highly structured.

The Spider's Guide to Predator Deception

by Elio

(left) An adult C. mulmeinensis. (right)
Decoys of prey pellets and egg sacs.
Source: Matt Walker, editor, Earth News.

We sometimes make a sally into the high jinks of metazoans, perhaps to persuade you that we are not prokaryotic chauvinists (not that you thought so, surely). This foray concerns a novel strategy that sheds light on an apparent paradox: many prey, instead of making themselves hard to see, seem to use tactics that make them easy for the predators to spot. To wit, certain fish, amphibians, reptiles, and insects are strikingly colored or are otherwise conspicuous, which poses a Darwinian paradox. The way out? Lure the predator into attacking a decoy! Here is a story of spiders that make spider decoys. And the decoys work.

A spider called Cyclosa mulmeinensis uses egg sacs and the leftover carcasses of its prey to make constructs that resemble its own body. These structures are strung along one of the guy wires of the web, which has earned this species the label Trash Line Spiders. Spider experts Ling Tseng and I-Min Tso of Tunghai University in Taiwan observed that parasitic wasps attacked the decoys more often than the spiders. The authors quantitated the cost and benefits of this behavior and concluded that this conspicuous antipredator display would enhance overall survival and was adaptive for this vulnerable prey. Thus, this strategy of fooling the predator rather than hiding from it seems to work. It may explain in part why so many spiders decorate their webs, something that has baffled arachnidologists for a long time. Sometimes in-your-face strategies work pretty well.

Location, Location, Location

Editors' Note: Never before in this blog's existence have we posted a point-by-point analysis of a research report. We are happy to begin a new tradition with Alan Derman's scholarly review of a major piece of work, the first bacterial "localisome" identifying the intracellular location of a large number of the proteins of Caulobacter. Of necessity, this is a longer article than most, but we suggest that you read it in its entirety, as it will acquaint you not only with the results of this study, but also with the issues involved in obtaining and deciphering the data.

by Alan Derman

Electron micrograph of a Caulobacter
predivisional cell prepared by negative
staining with uranyl acetate. Source.

Imagine trying to acquaint yourself with your favorite bacterium by learning the intracellular address of each and every one of its proteins. You can't see them in a light microscope, and you can't realistically do immunofluorescence; for that you'd need to purify each one and raise antibodies. So you have to modify them so that they can be seen. You have to tag them with a fluorescent tag such as green fluorescent protein (GFP), which means in the case of E. coli or B. subtilis, more than 8000 oligonucleotide primers, more than 4000 PCR amplifications, and as many clonings and transformations. And then when you have your more than 4000 or so strains, each one producing a distinct fluorescently tagged protein, you'll need to look at them all, one by one, under the fluorescence microscope, and record what you see. It's expensive, laborious, and time-consuming, and it's no wonder that it's been done for only three microorganisms. Two of these were yeast, the budding yeast S. cerevisiae, and the fission yeast S. pombe, which are more amenable to this kind of analysis than bacteria. Yeast cells are some 15 to 20 times larger in cross-sectional area than a conventional rod-shaped bacterium, and they conveniently contain discrete subcellular organelles to which proteins are localized. The third study did have E. coli for its subject. The proteins were tagged, but no systematic survey of their cellular locations was undertaken. The first bacterial "localisome" had yet to be constructed.

This was accomplished only recently, and not for E. coli but for the aquatic Gram-negative bacterium Caulobacter crescentus.

Talmudic Question #52

by Mark Martin

Given the ubiquity of intracellular associations between eukaryotes and prokaryotes, why are there so few reports of prokaryotes living "within" prokaryotes? In fact, I can only think of one reported case.

A Call From Arms

by Elio

Toyotomi Hideyoshi (1536 –1598). Source.

Towards the end of the 16^th century, the ruler of Japan, Toyotomi Hideyoshi, began a movement that led to the banning of firearms in that country. Not that these weapons hadn’t worked; on the contrary, at that time the Japanese made some of the best guns in the world. Many reasons have been put forward for this unique and drastic action, the most romantic being that the continued use of firearms would have undone the traditional role of the sword-wielding samurai. Now, microbes may not have such a convoluted social organization, but, when it comes to their making of antibiotics, there is something evocative of this remarkable chapter in history.

Antibiotics are now being thought about as benign compounds that, at least at low concentrations, have little to do with intraspecies warfare between organisms, and a great deal to do with the ways microbes communicate with one another. More and more examples are being reported of antibiotics that, at sub-inhibitory concentrations function, as community organizers, prodding bacteria into making protective biofilms. Indeed, antibiotic-induced biofilm formation has become the poster child for the argument that antibiotics serve mainly as signaling molecules between microbial cells. The evidence spans several bacterial species, including Staphylococcus aureus, Pseudomonas aeruginosa, Salmonella enterica, and Bacillus subtilis. Surely, other species will be found to be listening and to respond in other ways besides biofilm formation. Already the literature is rich and diverse. For some particularly juicy articles click here, here, here, here, or here.

Biology By the Numbers

by Elio

Did you ever need to look up the volume of a cell or the cellular concentration of ATP, only to find yourself spending much more time than you wanted on the Internet or flipping through textbooks—all without much success?

Well, it didn’t happen only to you. It is often surprising how difficult it can be to find concrete biological numbers, even for properties that have been measured numerous times. To help solve this for one and all, BioNumbers (The Database of Useful Biological Numbers) was created. It enables you to find in a minute (or less) any common biological number that might be important for your research, such as the rate of translation per ribosome, metabolite concentrations, or the number of bacteria in your gut. Along with the numbers, you'll find the relevant references to the original literature, useful comments, and related numbers.

BioNumbers is the product of two years of development, a joint effort by the systems biology department at Harvard Medical School and the Weizmann Institute in Israel, and currently draws over a hundred users daily. It is built as a collaborative, wiki-style, community effort. Each user can add new entries or comments, even ask for numbers that they couldn’t find—numbers needed for research or simply to satisfy curiosity. Curation is ensured by the requirement for a peer-reviewed reference followed by ongoing updating based on user feedback. Check it out here. Add a number. It might become the bion of the month.

Please send suggestions and comments to: ron.milo@weizmann.ac.il

Our thanks to Ron Milo for calling this to our attention.

The Genes, The Whole Genes, & Nothing But The Genes

by Merry

SEM of Oxytricha in the process of reproducing.
Source.

We have come to expect the unexpected of ciliates, and Oxytricha trifallax, with its genomic capers, does not disappoint. Like many of its more famous ciliate relatives (e.g., paramecium, tetrahymena, stentor), Oxytricha is a complex unicellular organism with many specialized cellular structures. Of course, they have the requisite cilia for locomotion, feeding, and sensing their environment. But they also have a "mouth," food vacuoles where digestion takes place, kidney-like contractile vacuoles for osmoregulation, and a pseudo-anus—the cytoproct. Not surprisingly, ciliates tend to be large cells, some measured in millimeters. Combined with a fast rate of growth, this may require more gene transcription than a diploid genome can support. To cope with this demand, ciliates employ a convoluted strategy, one unique so far to this group.

Of Terms in Biology: Sympatric & Allopatric

by Elio

These terms from biogeography are becoming relevant to us because of the present-day rise of microbiogeography. More and more, we hear about the "geographic" distributions of microbial species and strains.

Sympatric speciation means that two or more species arose from a population living within the same region, whereas allopatric tells you that physical separation was involved, with the species arising in different locales. Both terms derive from the Greek patra, homeland (as in patriotic). Sym denotes same, alike, or similar; allo, other.

Zebras and quaggas (some sympatric). Source.

For animals and plants, "homelands" may be readily defined, as in remote islands, atolls, patches of forest, etc. To microbiologists, the "homelands" can be harder to define. They may be as far-flung as continents, or as close as different segments of the human intestine. However the region is defined, the high rate of mutation and lateral gene transfer makes it easy for us to assume that a microbial species often arises sympatrically. All it takes is some variation in the selective factors operating within that ecological niche.

But these are oversimplifications and there is more to it. For a thorough and thoughtful explanation of these and related terms, see a timeless 2007 post, one of the Basic Concepts series in John Wilkins' splendid blog, Evolving Thoughts.

Playing the Light Organ Two Ways

The Hawaiian Bobtail Squid. Source.

by Elio

Deep within the oceans, sea animals and bioluminescent bacteria play symbiotic games. Fish, squid, and other animals that bring light to the darkness use it in their quest for food, their search for mates, or the avoidance of predators. This is not merely a curiosity, as seen by the simple fact that most animals living 2 km or more below the ocean surface are bioluminescent. One qualification: Not all of these bioluminescent animals depend on bacteria to generate light. Most do it all by themselves.

The usual way of thinking about these host-bacteria interactions has been straighforward: the host provides a site for the bacteria, the bacteria comply by making the light that is emitted from the animal. Actually, their interaction is not so simple. In the case of the well-studied Hawaiian Bobtail Squid, Euprymna scolopes, the host itself senses the light emitted by its symbionts, Vibrio fischeri— and not only with its eyes. Now, you ask, how does an animal perceive light other than by its eyes? It turns out that extra-ocular photodetectors are not uncommon among animals, this being but one example.