Small Things Considered

The Two Faces of Photorhabdus

by Merry

Heterorhabditis bacteriophora. Source.

Nematodes—those small, nondescript roundworms—are among the most numerous animals, found in virtually every ecological niche. With an estimated 400,000 to possibly 10,000,000 species, their diversity might match that of the insects, but no one knows for sure. Most nematodes live quiet lives, unknown even by taxonomists, but one—Caenorhabditis elegans—has made it big time as a model organism. Two families of entomopathogenic nematodes have garnered much attention due to the company they keep. (More about this below.) Some 350 million years ago, each family, it is thought, independently began a mutualistic association with a lineage of enteric bacteria—one with the lineage leading to the genus Photorhabdus, the other with the Xenorhabdus lineage. These nematode-bacterial teams are deadly parasitoids that prey on diverse insects. Both teams have evolved obligate mutualisms with similar life cycles, but the underlying molecular mechanisms are distinctly different. We'll focus on Photorhabdus luminescens, the most "illuminating" example. For a review article covering Xenorhabdus, click here.

A Personal Note: The Encyclopedia and I

by Elio

All things must be examined, debated, investigated without exception
and without regard for anyone's feelings.
            Diderot, 1713-1784. (one of the French Encyclopedists)

For the last couple of years, during hours not spent blogging, I served as the editor-in-chief of the third edition of the Encyclopedia of Microbiology. If this sounds like a large undertaking, it is. The work consists of nearly 300 entries compiled into six volumes that weigh in toto close to 50 lbs! Fortunately for those with weak backs, this edition will also be available electronically. My contribution to this project was reduced to human dimensions because practically all the work was done by an editorial board consisting of some terrific microbiologists. They chose the authors and edited the manuscripts. To see for yourself how distinguished these people are, click here. Did I critically read each entry from start to finish? Not on your life! (However, my curiosity was sufficiently piqued that I scanned—or more—each entry). Most of what I did was to cheer editors and authors along. I wasn't always good at this, but finally this Gargantuan creature emerged from its womb, hale and well.

No Phosphorus? No Problem! (There’s More Than One Way to Skin a Phytoplankton)

by Elio

Archaeal and Bacterial Lipids. Source.

Are you a lipophobe on a low fat diet? Or do you just believe that lipids are boring? Try again. Monotonous they are not. There’s greater variety to be found among the lipids than almost any other cell constituent. It’s truly mind-boggling. Within the prokaryotes alone, archaeal membrane lipids differ from “regular” ones in nearly every respect: they have ether rather than ester bonds between fatty acids and glycerol; hydrocarbon chains bound at the sn-2 and sn-3 positions of the glycerol; highly methyl-branched isoprenoid side chains; and, in some extremophiles, tails of the long chain isoprenoids fused to make a single tetraether lipid layer, thus belying the concept of the universal bilayered lipid membrane. Likewise, mycobacterial membranes contain a veritable zoo of unusual lipids. It goes on and on.

Talmudic Question #46

by Daniel Portnoy

Why don't mammals make antibiotics of the type so readily made by bacteria and fungi?

30,000 Parasitoids Can't Be Wrong

by Merry

Doomed. The tomato hornworm, the larva of the
hawk moth, Manduca quinquemaculata, is parasi-
tized by the braconid wasp Cotesia congregata
that lays dozens of eggs within each larva. When
fully mature, each wasp larva tunnels to the
outside of the caterpillar's body and spins a
whitish cocoon. Source.

Over 30,000 species of parasitoid wasps can't be wrong. Au contraire, their reproductive strategy has been highly successful. They deposit their eggs inside the larvae (or eggs) of other insects, typically lepidopterans (butterflies and moths). Although commonly called parasitic wasps, they qualify as “parasitoids” because parasitization is always deadly for the host. Normally, a caterpillar would recognize a foreign invader, such as a wasp egg, and activate its immune defenses to encapsulate the foreign object. The wasp prevents this by depositing venom and what looks to be viruses in the caterpillar along with her eggs. The venoms are chemically complex and act in a variety of ways to convert the caterpillar into a nursery for wasp larvae. In some species, the venom paralyzes the caterpillar and/or arrests its development prior to pupation. For the moment, we'll call those "viruses" virus-like particles (VLPs), a term used for particles that look like a virus but whose infectivity and components have not yet been characterized. The VLPs suppress the host immune response and are required for successful parasitization.

Fine Reading: HGT in Eukaryote Evolution

by Merry

The sea slug, Elysia chlorotica, retains
plastids from its otherwise digested algal
prey, Vaucheria litorea,, and the plastids
continue to photosynthesize for months.
At least one of the nuclear genes required
by the plastid was acquired by the sea
slug from the algae by HGT. Source.

Is horizontal gene transfer (HGT) a game for prokaryotes only, or can eukaryotes play, too? In their recent review of HGT in eukaryotes, Patrick Keeling and Jeffrey Palmer remind us:

Extant eukaryotes arose by HGT on the grandest scale possible—the endosymbiosis and subsequent genetic integration of entire organisms that gave rise to the mitochondrion and the plastid.

But, you say, that doesn't count. That may be a special case, two rare occurrences long, long ago. You want to know whether other genes, used by euks, have been acquired horizontally, and if so, when and from whom. Maybe even how. In this review, you'll find some intriguing examples that may send you off in pursuit of the referenced articles.

A Happy Hot Couple

by Elio

The southern end of the volcanic Kol-
beinsey Ridge with its isolated seamounts
perched on the Mid-Atlantic ridge north
of Iceland. Source.

We don't know about you, but we've become pretty blase about the stream of papers, each with the customary two dozen or more authors, reporting the completed genome of yet another microbe. But the recent one on the archaeon Ignicoccus hospitalis merits special attention. Combined with the previously sequenced genome of Nanoarchaeum equitans, we have a genomic window into one of the most exciting symbioses in the microbial world. We previously visited with this pair, and return now to continue their story.

This archaeal duo make up the only known obligatory ectosymbiosis among prokaryotes. There are symbioses aplenty between and among Bacteria and Archaea within the profusion of microbial communities on our planet. But in all those other cases, the partners have a somewhat casual physical association. Residing within multilayered biofilms or aggregates, metabolic partners might not even be touching. Here, the two are in intimate contact. One, the tiny N. equitans, requires its I. hospitalis "host" for survival—thus meeting the definition of obligatory.

Of Terms in Biology: Ortholog

Source.

The terms ortholog and paralog have wide acceptance. Yet, we find that they are used in nuanced ways by different people. Sure enough, here is some of what the Internet comes up with:

• ortholog: a gene from a disparate species, so similar in genetic sequence that it is assumed to have originated from a single gene in a common ancestral species.


• ortholog: either of two or more homologous gene sequences found in different species.


• orthologous: exhibiting orthology; having been separated by a speciation event.


• orthologs: homologous genes that result from speciation events (as opposed to paralogs, which result from duplication and subsequent divergence in a lineage).


• orthologous: groups of genes or proteins from different organisms that have the same function are said to be orthologous.


• orthologous: genes in different species are orthologous when their phylogeny is identical to the phylogeny of the species.

We deleted the ones that seemed like duplications (paralogs?). We find the first one most to our liking. Which do you think is most useful?

A Pathogen's Swiss Army Knife

by Maren von Köckritz-Blickwede

Mechanisms by which staph subverts innate immune defenses. Source

Staphylococcus aureus is an amazingly impressive bug that endlessly fascinates and worries microbiologists. It has an exceptional ability to exploit host immune functions, thereby causing a wide range of life­­­–threatening infections. For more than 40 years, new discoveries about its virulence potential have been made at a steadily increasing pace.