MyTH: Week 6 focus: Anaeromyxobacter spp.

This week I will write about bacteria that I dare say any of my readers know about, Anaeromyxobacter. Time again for My Tiny Highlight (MyTH). These bacteria were only recently discovered, first in Michigan but later in other sites. They are a peculiar member of a familiar group of bacteria, Myxococcus. Unlike the name suggests, Anaeromyxobacter can grow in the presence of oxygen, but they prefer anaerobic environments. They are found deep in the subsurface and can metabolize hazardous material for energy production similar to other deltaproteobacteria like Geobacter. Compounds in the environment that contain chlorine atoms are usually not a good thing. Luckily, Anaeromyxobacter can utilize these compounds to produce energy. Needless to say, Anaeromyxobacter are very versatile metabolically speaking since they can respire on 2-chlorophenol (or other halophenols), Uranium, iron, manganese, oxygen, nitrite, nitrate, nitrous oxide, and fumarate, to name a few. As far as metabolism goes, these bacteria are about as robust as they come. I personally have studied the genomes available for this genera of bacteria for a postdoc proposal. I can tell you, these guys are remarkable on many fronts.

First, Anaeromyxobacter have over half as many c-type cytochromes as the model Shewanella, 69 to 40. Cytochromes are the workhorses of metabolism that guide electrons towards the final electron acceptor like oxygen, iron, or uranium. Cytochromes accomplish this by shuttling electrons on heme groups. It is not uncommon for cytochromes to have multiple heme groups. Remarkably, Anaeromyxobacter has one cytochrome that has an astounding 40 heme groups. Shewanella cytochromes have  up to 10 hemes, to my knowledge.

What caught my eye was the number of PilZ domain proteins encoded within Anaeromyxobacter genomes. Four Anaeromyxobacter genomes have been sequenced: A. dehalogenans 2CP-C, 2CP-1, and FW105-9 as well as Anaeromyxobacter spp. K. Peeking into the genomes, all four are dead last in the number of enzymes that breakdown the bacterial second messenger molecule cyclic-di-GMP out of 1822 genomes that have at least 1 (they have 1 each). All four genomes are middle of the pack for the number of genes encoding enzymes to synthesis c-di-GMP with 10 (rank 989 out of 2032). Are you ready for this? Two of the four genomes contain 21 PilZ domain proteins (the binding domain of c-di-GMP). This is fourth among 1321 genomes which contain at least 1  PilZ protein; fourth most! The other two genomes are not that shabby at 18 and 13 PilZs each (rank 14 and 22 out of 1321 genomes, respectively).  Take a look at Table 1 to compare these numbers to the genomes of two model subsurface organisms from Geobacter and Shewanella.

Table 1: Annotated enzymes and receptor proteins for the bacterial second messenger cyclic-di-GMP in representative dissimilatory iron-reducing bacteria.

 Bacteria                                 DGCs                   PDEs                          PilZs

A. dehalogenans                     

2CP-C                          10 (989/2032)*    1 (1822/1822)             18 (14/1321)

2CP-1                          10 (989/2032)      1 (1822/1822)             21 (4/1321)

Fw105-9                     10 (989/2032)      1 (1822/1822)             13 (22/1321)

Anaeromyxobacter

K                                10 (989/2032)      1 (1822/1822)             21 (4/1321)

 G. lovleyi             43 (105/2032)      17 (1240/1822)            9 (53/1321)

S. oneidensis      51 (53/2032)         30 (43/1822)            4 (959/1321)

* indicates (genome rank/ total number of genomes containing at least one representative of the domain)

Based on annotations from MiST2 and Pfam proteome databases (http://mistdb.com/ and http://pfam.sanger.ac.uk/proteome/browse)

To me, this signifies that Anaeromyxobacter really rely heavily on sensing c-di-GMP to regulate their metabolism and lifestyle. This is especially true when you consider where in the genome the PilZ genes are found. For example, A. dehalogenans 2CP-C encodes 18 PilZ proteins. Several of the genes for these are in gene neighborhoods with nitrogen metabolism genes suggesting a genetic link between c-di-GMP sensing and nitrogen metabolism. I wish I could have studied these links between c-di-GMP signaling and metabolism in some capacity other than bioinformatically. However, those discoveries will have to go to the next chump in higher education.

110 different confirmations of cyclic-di-GMP

Related articles

• MyTH: A new weekly series about one bacterial species. First Post: Escherichia coli (mhrussel.wordpress.com)
• Taking the good with the bad: when beneficial bacteria do bad things on the side (mhrussel.wordpress.com)
• MyTH: Week 5 focus is Pseudomonas aeruginosa (mhrussel.wordpress.com)
• How do bacteria make decisions? Part 5: Mystery of a mysterious kind (mhrussel.wordpress.com)
• MyTH: Week 4 bacteria highlight: Geobacter spp. (mhrussel.wordpress.com)
• Animated bacteria GIF: What lies within (mhrussel.wordpress.com)

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