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Saturday, June 08, 2013

Strict Anaerobes that Produce Catalase

One thing every new bacteriology student learns on Day One is that some microbes are strict anaerobes (completely unable to use oxygen), and a universal characteristic of strict anaerobes is that they lack an important enzyme called catalase that breaks down hydrogen peroxide to oxygen and water. The idea is that anaerobes don't need to have catalase, because they don't live in the kind of highly oxidized environments where hydrogen peroxide forms. Lack of catalase is supposedly why many anaerobes are killed upon exposure to air. According to legend, once oxygen gets into the cells, hydrogen peroxide starts to build up, and with no catalase to break it down, anaerobes choke on toxic peroxides.

I'll let you in on a little secret, though. This nice-sounding story (about peroxide buildup killing anaerobes upon exposure to air) turns out to be mostly conjecture, not well supported by science. Even the bit about anaerobes lacking catalase isn't completely true. Many anaerobes do make catalase.

For today's post, I did a protein-sequence BLAST search against several families of obligate anaerobes using the katA gene of Proteus mirabilis as a reference, and I was quickly able to identify two dozen strict anaerobes that do, in fact, have a catalase gene (see table below).

Table 1: Strict Anaerobes that Produce Catalase
(tblastn query: Proteus mirabilis katA gene)

Organism
Length (AA)
E-value
Percent identities
Alkaliphilus metalliredigens strain QYMF
475
4.0E-97
40.0
Anaerococcus prevotii strain DSM 20548
473
2.0E-162
59.6
Anaerococcus vaginalis strain ATCC 51170
482
3.0E-171
61.4
Bacteroides coprocola strain DSM 17136
479
0
68.6
Bacteroides coprophilus strain DSM 18228
477
0
68.3
Bacteroides eggerthii strain 1_2_48FAA
478
0
69.6
Bacteroides intestinalis strain DSM 17393
478
0
70.0
Bacteroides ovatus strain 3_8_47FAA
478
0
69.0
Bacteroides plebeius strain DSM 17135
479
0
68.2
Bacteroides thetaiotaomicron strain VPI-5482
480
0
68.7
Clostridium botulinum A3 strain Loch Maree
341
4.0E-67
38.1
Clostridium botulinum B1 strain Okra
463
1.0E-67
33.9
Clostridium hathewayi strain WAL-18680
474
7.0E-167
58.6
Clostridium lentocellum strain DSM 5427
476
2.0E-168
59.4
Clostridium phytofermentans strain ISDg
472
3.0E-107
43.6
Desulfitobacterium dichloroeliminans strain LMG P-21439
477
0
72.3
Desulfitobacterium hafniense DCB-2
493
1.0E-100
39.9
Desulfosporosinus youngiae strain DSM 17734
491
7.0E-103
41.1
Desulfotomaculum ruminis strain DSM 2154
477
2.0E-142
52.2
Dethiobacter alkaliphilus strain AHT 1
468
5.0E-102
40.3
Lachnospiraceae bacterium strain 3_1_57FAA_CT1
470
1.0E-165
59.5
Propionibacterium acnes strain 266
444
3.0E-114
47.2
Syntrophobotulus glycolicus strain DSM 8271
484
2.0E-102
40.7
Veillonella sp. strain 3_1_44
474
0
66.0

Each entry in this table represents a protein-sequence (not DNA sequence) match between a gene in the organism listed and the catalase gene of Proteus mirabilis. (Proteus is a facultative anaerobe related to E. coli and Salmonella.) The length of each organism's catalase enzyme, in amino acids, is shown under Length. (By way of reference, the Proteus catalase is 484 amino acids long.) E-value is the so-called expectation value, a measure of how likely the sequence match would be by chance. All of the values shown are extraordinarily low. "Percent identities" is the percentage of amino-acid matches between the Proteus enzyme and the target organism's enzyme. Values in the 30% to 40% range are not unusual for functionally related enzymes in otherwise distantly related organisms. Values above 60% tend to suggest a phylogenetic relationship, whereas in two organisms that are known to be unrelated, a value above 70% would (in many cases) be considered evidence of possible horizontal gene transfer. 

Here's the protein-blast query sequence I used, in case you want to verify these results (or go looking for more catalase-producing anaerobes):

>Proteus mirabilis strain HI4320(v1, unmasked), Name: PMI1740, YP_002151471.1, katA, Type: CDS, Feature Location: (Chr: 1, 1861974..1863428) Genomic Location: 1861974-1863428
MEKKKLTTAAGAPVVDNNNVITAGPRGPMLLQDVWFLEKLAHFDREVIPERRMHAKGSGAFGTFTVTHDITKYTRAKIFSEVGKKTEMFARFSTVAGER
GAADAERDIRGFALKFYTEEGNWDMVGNNTPVFYLRDPLKFPDLNHIVKRDPRTNMRNMAYKWDFFSHLPESLHQLTIDMSDRGLPLSYRFVHGFGSHT
YSFINKDNERFWVKFHFRCQQGIKNLMDDEAEALVGKDRESSQRDLFEAIERGDYPRWKLQIQIMPEKEASTVPYNPFDLTKVWPHADYPLMDVGYFEL
NRNPDNYFSDVEQAAFSPANIVPGISFSPDKMLQGRLFSYGDAHRYRLGVNHHQIPVNAPKCPFHNYHRDGAMRVDGNSGNGITYEPNSGGVFQEQPDF
KEPPLSIEGAADHWNHREDEDYFSQPRALYELLSDDEHQRMFARIAGELSQASKETQQRQIDLFTKVHPEYGAGVEKAIKVLEGKDAK

ADDENDUM: After writing this post, I found that catalase also occurs in archeons. See this post for details.

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