Small Things Considered

Promiscuous Bacteria and Viral Playboys

by Merry

Picasso's vision of licentiousness. Source.

Bacteria have been sexually promiscuous, swapping genes with gusto, for a very long time. More than 15% of E. coli's genome has arrived via horizontal gene transfer (HGT), with some 200 installments having turned up since it diverged from Salmonella 100 million years ago. And, as you are probably thinking, those 200 are but the tip of the HGT iceberg, the small fraction of transfers that were useful enough to be not only maintained by the recipient but also to spread through the population. But how much of this gene transport is the work of viruses?

Virus-mediated transduction is but one of the three major mechanisms that bacteria use to pick up genes, the other two being conjugation and transformation. The rates of transduction as conventionally measured for freshwater and marine ecosystems have been highly variable but always low, ranging from 10^-11 to 10^-5 transduced bacteria per phage (i.e., per plaque-forming unit or PFU). However, there being such huge numbers of phages, even these low rates lead to large numbers of transferred genes. Some 10¹⁴ bacteria in Tampa Bay and 10¹³ in the Mediterranean basin garner genes this way each year. Because they thought that these measured rates are way low, a group of Japanese researchers developed a new methodology for measuring the frequency of phage-mediated gene transfer.

Talmudic Question #62

What if all prokaryotic plasmids on this planet went on strike and refused to have their genes expressed?

Retrospective, May 2010

As is our tradition, we present here a lightly annotated list that includes most of our posts from the past half year.

Phage Epsilon15 at a resolution of 4.5 Ǻ. Source.

Viruses

Viral Turtles. Viruses with dsRNA genomes enter host cells, capsid and all, and then keep their capsid intact as a safe workshop in which to transcribe their genes. A neat strategy for evading host defenses!

Paleovirology. Associate blogger Welkin Johnson takes along on a historical tour of the endogenous retroviruses of mammals, and from there it is but a short hop to the surprising recent discovery of Bornavirus sequences in the human genome.

A Most Lively Virus. How about that? A virus that sprouts two l-o-n-g tails all on its own, after exiting from its host. Just another one of those wonders from the world of hyperthermophilic archaea and their viruses.

A Holin One. Holins, phage-encoded enzymes that lyse the host cell by making holes in the membrane, don't just make small pores. They make huge fissures that allow other phage enzymes to rapidly attack the cell wall and let the phages out.

Time’s Up. Phage infections are precisely orchestrated, even to timing the moment of cell lysis. We visit holin-land, and there learn that these small proteins end the game at just the right time.

Prophage Masquerade. Does that bacterium have any prophages on board? Not an easy question to answer. Prophages come in various forms, some inducible and some not. Some may even have been co-opted by their host and put to work as gene transfer agents for their genes.

Five Questions About Lysogeny. We found some intriguing answers to our questions. Lysogeny can benefit both phage and host, and may even play a key role in microbial evolution.

Symbiosis

Source.

Autumn Leaves. Leaves of your favorite tree are turning yellow, thus shutting down your pantry (if you’re a caterpillar ensconced inside a leaf). What to do? Use your endosymbiotic Wolbachia to produce cytokines that keep an island of the leaf green (and nutritious).

Leaf-Cutters Get Their Fix (nitrogen fix, that is). You know that leaf-cutting ants are terrific at eating the fungi they cultivate in their gardens. But where do they get their nitrogen from? Could it be from nitrogen-fixing bacteria? Looks that way.

Genomics

And The Winner Is… The most abundant gene in the known universe? Transposase!

Source: Museum of the History of
Science, Oxford.

History

Did van Leeuwenhoek Observe Yeast Cells in 1680? Nanne Nanninga examined letters and other historical material, then concluded that “our founder” actually saw yeast cells in his beer.

A Matter of Timing: Yellow Fever and the Mosquito Hypothesis. Associate blogger Welkin Johnson leads us through the maze of how yellow fever is transmitted and points to the role that this discovery played in the birth of modern virology.

A Close Encounter of the Enological Kind. John Ingraham regales us with a story of how he discovered the wine taste-correcting bacterium, Oenococcus oeni, of malolactic fermentation fame.

How Proteomics Got Started. The first to use proteomics to study bacterial physiology, Fred Neidhardt shares with us tales from those early days.

Source.

Pathogens

All Is Fair in Love and Warfarin. Graduate students Shigeki Miyake-Stoner and Spencer Diamond found it exciting that tubercle bacilli have a homologue of a protein called Vitamin K epoxide reductase, the target for warfarin. Sure enough, this drug affects the growth of M. tuberculosis.

Eukaryotes

Naegleria’s Split Morphology Disorder. Borrowed from the blog Skeptic Wonder by Psi Wavefunction is this tantalizing description of the cellular shenanigans of Naegleria that enjoys changing from an amoeba to a flagellate in a short two hours.

Mother’s Love. Budding yeasts have an advantage over cells that divide by mere binary fission: the bud and the mother cell are distinctive physical entities with different fates. Damaged proteins are removed from the buds and sequestered in the mother cells.

True or False: All Metazoans Need O₂. False. Small metazoans called Loricifera thrive in an anaerobic brine lake at the bottom of the sea off Crete.

Physiology & Cell Structure

From the Latent Utopias exhibition from the
Steirischer Herbst in Graz, Austria. Source.

Everyone Rowing in the Same Direction. We revisit the multicellular prokaryotes, this time focusing on the recently-described group that navigates by negative phototaxis rather than magnetotaxis.

When Crenarchaeota Divide, They Multiply. Graduate students Jenn Tsau and Suzy Szumowski tell us of another archaea-eukarya connection: they both have ESCRT proteins. In eukaryotes, these act as an “endosomal sorting complex required for transport,” but in some archaea they may participate in cell division.

On the Continuity of Biological Membranes. Frank Harold, whose concepts of the cell have influenced the thinking of many, has graced our pages with another insightful and discerning essay on the origin of membranes. A must read, if you missed it before!

Of Archaeal Periplasm & Iconoclasm. Elio likes to think he is an iconoclast, and he is in good microbial company. Counted among the iconoclasts surely would be the thermophilic archaeon Ignicoccus hospitalis, which has energy producing-machinery on the outer of its two membranes.

Measuring the Strength and Speed of the Microbial Grappling Hook. Graduate student Amber Pollack-Berti (the blogger of Tiny Topics) describes how to measure the force exerted by a bacterium when it retracts its Type IV pili.

Through the Looking Glass: Silicate in Bacterial Spores. Silica and anthrax—sounds familiar? Weaponized spores? Peter Setlow explains that silicates are found naturally on such spores.

Mysteries of the Bacterial L–Form: Can Some of Them Be Unveiled? Hans Martin enlightens us about the mysterious survival abilities of these aberrant bacterial forms. They seem to make some peptidoglycan in the presence of penicillin, using drug-resistant enzymes.

Kryptonian Vision. Frequent contributor to this blog, grad student Jennifer Gutierrez explains (somewhat heroically) how an X-ray microscope works and what we might be able to see with X-ray vision.

Source.

Ecology

You Are What You Eat. Eat seaweeds and you're apt to have gut bacteria that have acquired genes for the enzymes needed to digest their unique polysaccharides. So write graduate students Karen Schwarzberg and Mike Gurney.

Cryptic Life in the Antarctic Dry Valleys. We contemplate the microbial life in the most barren of lands in Antarctica. A surprisingly diverse group of stalwart organisms eke out a sheltered existence within the crevices of the rocks, and even beneath translucent stones.

Source.

Odds & Ends

State Microbes. In the wake of Elio's interviews on National Public Radio‘s All Things Considered about official state microbes, we’re having fun hearing from readers which microbes they deem most suited for their state (or city or country). Our favorite? Actually a “City Microbe,” Clostridium botulinum, for Los Angeles, for providing botox to embellish the locals.

The Attendee's Guide to Scientific Meetings, Part II. A second installment from Julian Davies counseling us on how to survive (and even thrive) at large meetings. Good advice presented in a humorous capsule.

Of Terms in Biology: Gene Ontology. The au courant bioinformatics-savvy phylogenomicist knows that this is how you categorize all that information.

Everyone Rowing in the Same Direction

by Merry

Source.

Is there such a thing as an obligatorily multicellular prokaryote? We presented a case for their existence before, one that fueled our evolutionary imaginations. Unlike the myxobacteria, for example, which have both unicellular and multicellular stages, some magnetotactic bacteria appeared to be multicellular throughout their lives. Their multicellular coordination is apparent from their complex swimming behavior, their synchronous cell division, and their subsequent division into two equal multicellular spheres. Intriguing they are, but they could easily be relegated onto a shelf for microbial oddities—just one small group within the δ-proteobacteria, magnetotactic and restricted to saline environments.

Differential interference contrast (DIC) light micro-
graph of a disaggregated nMMP. Source.

Now a recent paper announces the finding of a new subgroup within that multicellular clade. These new critters have a similar life cycle and morphology. They, too, are sulfate-reducers, but they are found in low-saline, nonmarine aquatic environments, and they are not magnetotactic—thus called non-Magnetotactic Multicellular Prokaryotes or nMMPs. Although they don't navigate by compass, they do exhibit active negative phototaxis—the first δ-proteobacteria known to do so. This ability was useful for the researchers; they set up a "light racetrack" in a capillary tube to concentrate these unculturable bacteria at one end of the tube. Is phototaxis useful for the nMMPs?

You Are What You Eat

B. plebeius, the recipient of the β-porphyranase
genes. Source.

by Karen Schwarzberg and Mike Gurney

Despite the rise of a global culture, deliciously distinct differences in diet still persist among various nationalities. Makes one wonder if, along with each cuisine, comes a distinctive microbiome. We now have the research tools needed to begin to explore such possibilities. A paper recently published in Nature by Hehemann et al. reports that, in at least one particular instance, we do harbor bacteria adapted to the traditional diet of our culture.

Nori au naturel. Source.

All of us humans rely on our gut bacteria to supply enzymes that we lack but that we need in order to digest the polysaccharides found in terrestrial plants. But the enzymes (glycoside hydrolases) needed to breakdown polysaccharides unique to marine algae, such as carrageenan and agar, are another story. Such enzymes had been identified only in some marine bacteria. Hehemann and colleagues wondered about the Japanese, who consume, on average, 14 grams of seaweed per day (mostly the Porphyra spp. of red algae known as nori). Nori contains the sulphated polysaccharide porphyran, so they began their investigation by searching for porphyranases within the genome sequence of a marine Bacteroidetes that lives on another red alga, Zobellia galactanivorans. Sure enough, they found two such enzymes (β-porphyranases). Structure analysis provided knowledge of the active site, making it possible to mine for more porphyranases in the GenBank non-redundant database. This netted them six more likely β-porphyranases. All of these enzymes were from marine bacteria with the exception of one found in Bacteroides plebeius, a human gut bacterium. Notably, all 6 strains of B. plebeius described so far have been isolated from the microbiota of Japanese individuals. This includes the type strain that was sequenced as part of the Human Microbiome Project.

Welcome, mBio

by Elio

ASM has announced the launch of mBio™, the Society’s first broad-scope, open-access online journal (which means it can be accessed for free). Readers can get an inside glimpse of the latest via mBiosphere, the journal’s blog run by Merry Buckley. (What were the chances of two Merrys writing blogs for the ASM?) Arturo Casadevall, the Founding Editor-in-Chief, says the new journal is a good choice for scientists who wish to publish cutting-edge research quickly.

mBio is published in association with the American Academy of Microbiology, the honorific leadership group within the ASM. The Academy’s mission is to recognize scientists for outstanding contributions to microbiology, which is in synch with mBio’s mission to publish high-quality articles across the entire field of microbiology. Here’s a sample of work that will be reported in the inaugural issue of mBio that will be online in mid-May:

• a way to produce a disease state in infant rabbits much like human cholera.
• progress toward the goal of an influenza virus vaccine that would protect against multiple strains
• identification of numerous targets across the entire E. coli chromosome to which SeqA binds
• the first evidence for a biofilm cell protein that senses the presence of completion of synthesis extracellular matrix
• demonstration of the existence of ~1,000 antisense RNAs in E. coli, which may represent an important but overlooked class of regulatory molecule
• two major new papers on Cryptococcus neoformans, an AIDS-associated human fungal pathogen
• an intriguing essay proposing that global preparedness for the effects of climate change should consider the possibility of an increased prevalence of fungal diseases in mammals

We wish this new journal much success.

Viral Turtles

by Merry

Source.

A double stranded RNA (dsRNA) viral genome, introduced into a host cell, is met by formidable host defenses. The very presence of dsRNA in a eukaryotic or prokaryotic cell announces a viral infection and elicits effective responses, ranging from silencing of the viral mRNAs to apoptosis. Despite that, there are successful dsRNA viruses throughout the biosphere. By 2000, eight families with close to 200 "species" were known to infect bacteria, fungi, plants, and animals. The broad diversity of their hosts notwithstanding, all dsRNA viruses share the same secret to success: they bring their capsid into the cell along with their genome to serve as a safe compartment where they transcribe and replicate their genome. Their dsRNA is never exposed.

For the virus whose virion is but a simple protein capsid, it is the entire virion that enters and persists intracellularly. For others that have additional outer layers of protein and/or a membrane, those layers are removed during cell entry and the inner capsid alone enters the cytoplasm. The outer layers vary greatly from group to group, presumably reflecting adaptations to particular hosts or modes of transmission, while the proteins of the inner capsid, as well as its architecture, are highly conserved among all dsRNA viruses. Doesn't this suggest a common ancestry?

This strategy poses particular challenges, not the least of which is how do you transport something as large as a virion across the cell membrane. Also, since a dsRNA genome is not a suitable template for protein translation or for cellular replicases, these viruses have to bring their own RNA-dependent RNA polymerase (RdRp) with them. The capsid itself has to be selectively porous, allowing nucleotides to enter and RNA transcripts to exit.

State Microbes

by Elio

Not long ago, I was interviewed twice (click here and here) by Michelle Norris of National Public Radio’s All Things Considered regarding the burning issue of state microbes. The first interview was in response to the news that the state of Wisconsin’s State Assembly passed a bill proclaiming Lactococcus lactis as its state microbe. I opined that this would be a most appropriate choice, given the role of this bacterium in making cheese, a matter of obvious importance to Wisconsinites. Alas, the state Senate did not take up the bill, so L. lactis will have to wait (perhaps in a lyophilized state) for future proposals. Michelle proposed that the other states now have the chance to be the first to adopt a state microbe. Listeners sent in their nominations, some of which we discussed during the second interview.

Mentioning the quest for state microbes to microbiologists and non-microbiologists alike usually results in a chuckle. Fair enough: in today’s world, preoccupation with such ostensibly trivial matters may be frivolous. Still, there could be an educational point to this. Kids in each state, when presented with the state microbe, may want to figure out what makes the microbe special and even learn something about microbes in general. (Maybe adults, too!)

The interviews were good fun (the kinship in the names of our respective activities, STC and ATC, was a comfortable point of departure). Michelle was exceedingly friendly and helpful, likewise her off-the-air colleague Melissa Grey (author of All Cakes Considered). Both were eager to delve into matters microbial. Each time the interview lasted some 15 minutes, from which they selected the material that was aired. We chatted in a free and easy manner that I found both relaxed and pleasant.

Here is a list of nominations from NPR listeners and readers of New Scientist, as well as some of our own. Perhaps microbiologists in each state will find it worthwhile to come up with their choices. Those with political connections to state legislators should pay special heed. I omit suggestions of pathogenic agents (with a couple of exceptions), on the supposition that state legislatures would not take kindly to them.

• Alabama: Karenia brevis, a dinoflagellate, aka the Red Tide Alga. A shoo-in if you think of the Crimson Tide. (Jenny Ridings, New Scientist)
• Alaska: The permafrost bacterium Carnobacterium pleistocenum found in 35,000 year-old ice. (Rowan Hooper, news editor, New Scientist)
• Arizona: (1) Thiobacillus ferrooxidans for its role in copper leaching. Arizona is the top copper-producing state in the US. (Elio)
(2) Penicillum for the penicillin it makes, to be used to cure gunshot wounds due to the recent illegal immigrant law. (NPR listener)

• California: (1) Saccharomyces cerevisiae, for its importance in making wine. (Elio) (Also suggested for several other states)
(2) The city of Los Angeles got two nominations for a “city microbe:” Clostridium botulinum, the source of botox. (NPR listener; Rowan Hooper, news editor, New Scientist)

• Florida: (1) Retirement communities in Florida would appreciate the 250-million-year-old Lazarus bacillus Bacillus permians. Note that there is far from universal agreement about the longevity of this bacterium. (Rowan Hooper, news editor, New Scientist)
(2) The Sunshine State can share its ample sunlight and coastal waters with a photosynthetic marine cyanobacterium, e. g., Synechococcus elongatus. (Elio)

• District of Columbia: Cupriavidus metallidurans (formerly Ralstonia metallidurans), the gold mining bug that turns soluble gold into nuggets. They could use it there. See our previous post. (Elio)
• Hawaii: Another state claiming Lactococcus lactis, here fermenting taro into poi. (Merry)
• Indiana: Zymomonas mobilis, a bacterium that produces ethanol very efficiently. Indy 500 cars run on ethanol. (AmoebaMike, New Scientist)
• Iowa: Bradyrhizobium japonicum, a nitrogen fixing symbiont of soybean plants. Iowa is one of the top soybean producers in the US. (Elio)
• Kansas: MRSA, for illustrating evolution in action. (several NPR listeners)
• New Jersey: (1) Streptomyces griseus, the bacterium that makes streptomycin, a pioneer antibiotic discovered at Rutgers University by Selman Waxsman. (Elio)
(2) Sewage methanogenic bacteria, for New Jersey’s famous marshland garbage dumps. (Rowan Hooper, news editor, New Scientist)

• New Mexico: The “indestructible bacterium” Deinococcus radiodurans that probably survived the Trinity A bomb test carried out in New Mexico in 1945. (Rowan Hooper, news editor, New Scientist)
• Nevada: Home of the neon glow in Las Vegas gets the flashing light of Vibrio fischeri. (Rowan Hooper, news editor, New Scientist)
• Rhode Island (1) Epulopiscium fischelsoni, the biggest known bacterium (never mind Thiomargarita) for the smallest state in the Union. (NPR listener)
(2) The nanobacteria (Ed. Note: assuming they exist). (Rowan Hooper, news editor, New Scientist)

• Texas: The oil eating Synthropus may be useful for cleanup of oil spills. (Rowan Hooper, news editor, New Scientist)
• Utah: The salt-loving Haloarcula for the Great Salt Lake. (Rowan Hooper, news editor, New Scientist)
• Virginia: The Epstein Barr virus or kissing bug because “Virginia is for lovers.” (NPR listener)
• Washington: Here they may appreciate the rain-making bacterium Pseudomonas syringae. (Rowan Hooper, news editor, New Scientist)
• Wisconsin: Lactococcus lactis, the essential cheese-maker. (Wisconsin State Assembly)
• Wyoming: Thermus aquaticus, which was isolated from a Yellowstone hot spring and went on to make a great living as the source of the Taq polymerase. (Elio)

Can you think of others? Keep them coming!

Mysteries of the Bacterial L-Form: Can Some of Them Be Unveiled?

by Hans H. Martin

Figure 1. Peptidoglycan sacculi isolated from L-form
spheroplasts of P. mirabilis. Electron micrograph of
Pt-Ir-shadowed sample. 20,000X.

L-forms are bacterial variants with defective cell walls and irregular growth and multiplication. They arise after peptidoglycan, the exoskeleton of the bacterial cell wall, has been either degraded by bacteriolytic enzymes, or its biosynthesis has been disturbed by antibiotics and other inhibitors, or by defect mutations in essential genes for cell wall synthesis. L-forms with different degrees of wall defects can arise. International experts, headed by nobelist Sidney Brenner, recognized the need to distinguish between entirely cell wall-less protoplasts, surrounded only by a cytoplasmic membrane, and spheroplasts with residual, fragile cell walls. L-forms were discovered in 1935 by Emmy Klieneberger and subsequently described by many authors (examples here and here). Much interest in L-forms arose from their assumed but still unconfirmed roles as concealed pathogens and as survivors of antibiotic action. They are also useful tools for the study of basic mechanisms of cell biology, such as cell division. Yet, as justly deplored in a recent review, L-forms are still "unfamiliar to many microbiologists" and are often regarded "with scepticism." One hears complaints about the unusually labor-intensive and time-consuming process of L-form isolation and cultivation, and the uncertain outcome. However, in my experience, this can be overcome by patient determination.

A special type of resistance to antibiotics, which we studied extensively in my lab, is reflected in the ability of the Gram-negative bacterium Proteus mirabilis to evade the inhibitory action of penicillin and other β-lactam antibiotics by growing as spheroplast- L-forms (references here and here). It is important to note that the most common resistance mechanism, inactivation of β-lactam antibiotics by β-lactamase, is not involved in this phenomenon.