Viral abduction of proteins

I have to admit, when I first saw the paper by Newcomb and Brown called "Internal Catalase Protects Herpes Simplex Virus from Inactivation by Hydrogen Peroxide" (J. Virology, 2012, 86:21; full article here), I was tempted to dismiss it as a fluke. What Newcomb and Brown found is that herpes virus appears to contain a fully functioning version of the enzyme catalase. This enzyme, which is present in human cells and, in fact, most aerobic life forms (but also some anaerobes), breaks down hydrogen peroxide to molecular oxygen and water. It detoxifies hydrogen peroxide, if you will.

Herpes simplex virus components.

The odd thing about herpes virus containing catalase is that the herpes genome does not contain a gene for catalase (and this is acknowledged by Newcomb and Brown). Thus, any catalase present in the virion has to have been made by the host cell. The enzyme is piggybacking a ride inside the virion.

It appears that, far from being a fluke, the herpes virus tegument proteins (proteins that lie just underneath the capsid proteins that make up the outer shell of the virion) have evolved in such a way as to attract or stick to catalase, sucking it along for the ride.

Having catalase on board brings survival benefit to the virus. According to Newcomb and Brown:

HSV-1 [herpes virus] was found to be more sensitive to killing by hydrogen peroxide in the presence of a catalase inhibitor than in its absence. The results suggest a protective role for catalase during the time HSV-1 spends in the oxidizing environment outside a host cell. 

In what sense would catalase protect the virus? Peroxides are damaging to DNA, and herpes is a DNA virus. Where do peroxides come from? Short answer: phagocytes (think white blood cells). When a phagocyte ingests bacteria (or any material), its oxygen consumption increases. The increase in oxygen consumption, called a respiratory burst, produces reactive oxygenated species (nitric oxide, superoxides, hydrogen peroxide), which are toxic to most life forms, unless (of course) detoxifying enzymes come into play. In this case, herpes comes well-prepared for the confrontation. It brings copies of the host's own catalase.

This is an extremely clever adaptation (if that's what it is). If you're a virus, why go to the trouble of adding a dedicated catalase gene to your DNA if you can simply recruit host catalase into the capsid by suitable modification of a tegument protein?

Arenavirus can capture ribosomes in virions.

Selective entrainment of host proteins is not unknown in viruses (it's been well studied in HIV and in vesicular stomatitis virus, for example). Even in the case of catalase, it's been known since 1938 that vaccinia virus, a relative of smallpox, carries with it the host's own catalase.

Perhaps the most extreme (and startling) example of viral recruitment of host proteins into virions is provided by Arenavirus (an agent of aseptic meningitis in humans), which can package up host-cell ribosomes (see photo).

It could very well be that most large viruses, such as NCLDVs (and mid-size viruses as well; herpes is by no means large), routinely package host enzymes in their virions. As modern proteomic techniques are brought to bear on the study of virion-associated host proteins, we can probably expect many additional discoveries of this sort in the near future.

More Science on the Desktop

If you took Bacteriology 101, you were probably subjected to (maybe even tested on) the standard mythology about anaerobes lacking the enzyme catalase. The standard mythology goes like this: Almost all life forms (from bacteria to dandelions to humans) have a special enzyme called catalase that detoxifies hydrogen peroxide by breaking it down to water and molecular oxygen. The only exception: strict anaerobes (bacteria that cannot live in the presence of oxygen). They seem to lack catalase.

I've written on this subject before, so I won't bore you with a proper debunking of all aspects of the catalase myth here. (For that, see this post.) Right now, I just want to emphasize one point, which is that, contrary to myth, quite a few strict anaerobes do have catalase. I've listed 87 examples by name below. (Scroll down.)

I have to admit, even I was shocked to find there are 87 species of catalase-positive strict anaerobes among the eubacteria. It's about quadruple the number I would have expected.

If you're curious how I came up with a list of 87 catalase-positive anaerobes, here's how. First, I assembled a sizable (N=1373) list of bacteria, unduplicated at the species level. (So in other words, E. coli is listed only once, Staphylococcus aureus is listed only once, etc. No species is listed twice.) I then used the free/online CoGeBlast tool to run two Blast searches: one designed to identify aerobes, and another to identify catalase-positive organisms. In the end, I had all 1,373 organisms tagged as to whether each was aerobic, anaerobic, catalase-positive, or catalase-negative.

It's not as easy as you'd think to identify strict anaerobes. There is no single enzymatic marker that can be used to identify anaerobes reliably (across 1,373 species), as far as I know. I took the opposite approach, tagging as aerobic any organism that produces cytochrome c oxidase and/or NADH dehydrogenase. (These are enzymes involved in classic oxidative phosphorylation of the kind no strict anaerobe participates in.) In particular, I used the following set of amino acid sequences as markers of aerobic respiration (non-biogeeks, scroll down):

>sp|Q6MIR4|NUOB_BDEBA NADH-quinone oxidoreductase subunit B OS=Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100) GN=nuoB PE=3 SV=1
MHNEQVQGLVSHDGMTGTQAVDDMSRGFAFTSKLDAIVAWGRKNSLWPMPYGTACCGIEF MSVMGPKYDLARFGAEVARFSPRQADLLVVAGTITEKMAPVIVRIYQQMLEPKYVLSMGA CASSGGFYRAYHVLQGVDKVIPVDVYIPGCPPTPEAVMDGIMALQRMIATNQPRPWKDNW KSPYEQA
>sp|P0ABJ3|CYOC_ECOLI Cytochrome o ubiquinol oxidase subunit 3 OS=Escherichia coli (strain K12) GN=cyoC PE=1 SV=1
MATDTLTHATAHAHEHGHHDAGGTKIFGFWIYLMSDCILFSILFATYAVLVNGTAGGPTG KDIFELPFVLVETFLLLFSSITYGMAAIAMYKNNKSQVISWLALTWLFGAGFIGMEIYEF HHLIVNGMGPDRSGFLSAFFALVGTHGLHVTSGLIWMAVLMVQIARRGLTSTNRTRIMCL SLFWHFLDVVWICVFTVVYLMGAM 
>sp|Q9I425|CYOC_PSEAE Cytochrome o ubiquinol oxidase subunit 3 OS=Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) GN=cyoC PE=3 SV=1
MSTAVLNKHLADAHEVGHDHDHAHDSGGNTVFGFWLYLMTDCVLFASVFATYAVLVHHTA GGPSGKDIFELPYVLVETAILLVSSCTYGLAMLSAHKGAKGQAIAWLGVTFLLGAAFIGM EINEFHHLIAEGFGPSRSAFLSSFFTLVGMHGLHVSAGLLWMLVLMAQIWTRGLTAQNNT RMMCLSLFWHFLDIVWICVFTVVYLMGAL
>tr|Q7VDD9|Q7VDD9_PROMA Cytochrome c oxidase subunit III OS=Prochlorococcus marinus (strain SARG / CCMP1375 / SS120) GN=cyoC PE=3 SV=1
MTTISSVDKKAEELTSQTEEHPDLRLFGLVSFLVADGMTFAGFFAAYLTFKAVNPLLPDA IYELELPLPTLNTILLLVSSATFHRAGKALEAKESEKCQRWLLITAGLGIAFLVSQMFEY FTLPFGLTDNLYASTFYALTGFHGLHVTLGAIMILIVWWQARSPGGRITTENKFPLEAAE LYWHFVDGIWVILFIILYLL
>sp|Q8KS19|CCOP2_PSEST Cbb3-type cytochrome c oxidase subunit CcoP2 OS=Pseudomonas stutzeri GN=ccoP2 PE=1 SV=1
MTSFWSWYVTLLSLGTIAALVWLLLATRKGQRPDSTEETVGHSYDGIEEYDNPLPRWWFM LFVGTVIFALGYLVLYPGLGNWKGILPGYEGGWTQVKEWQREMDKANEQYGPLYAKYAAM PVEEVAKDPQALKMGGRLFASNCSVCHGSDAKGAYGFPNLTDDDWLWGGEPETIKTTILH GRQAVMPGWKDVIGEEGIRNVAGYVRSLSGRDTPEGISVDIEQGQKIFAANCVVCHGPEA KGVTAMGAPNLTDNVWLYGSSFAQIQQTLRYGRNGRMPAQEAILGNDKVHLLAAYVYSLS QQPEQ
>sp|P57542|CYOC_BUCAI Cytochrome o ubiquinol oxidase subunit 3 OS=Buchnera aphidicola subsp. Acyrthosiphon pisum (strain APS) GN=cyoC PE=3 SV=1
MIENKFNNTILNSNSSTHDKISETKKLFGLWIYLMSDCIMFAVLFAVYAIVSSNISINLI SNKIFNLSSILLETFLLLLSSLSCGFVVIAMNQKRIKMIYSFLTITFIFGLIFLLMEVHE FYELIIENFGPDKNAFFSIFFTLVATHGVHIFFGLILILSILYQIKKLGLTNSIRTRILC FSVFWHFLDIIWICVFTFVYLNGAI
>sp|O24958|CCOP_HELPY Cbb3-type cytochrome c oxidase subunit CcoP OS=Helicobacter pylori (strain ATCC 700392 / 26695) GN=ccoP PE=3 SV=1
MDFLNDHINVFGLIAALVILVLTIYESSSLIKEMRDSKSQGELVENGHLIDGIGEFANNV PVGWIASFMCTIVWAFWYFFFGYPLNSFSQIGQYNEEVKAHNQKFEAKWKHLGQKELVDM GQGIFLVHCSQCHGITAEGLHGSAQNLVRWGKEEGIMDTIKHGSKGMDYLAGEMPAMELD EKDAKAIASYVMAELSSVKKTKNPQLIDKGKELFESMGCTGCHGNDGKGLQENQVFAADL TAYGTENFLRNILTHGKKGNIGHMPSFKYKNFSDLQVKALLNLSNR
>sp|P0ABI8|CYOB_ECOLI Ubiquinol oxidase subunit 1 OS=Escherichia coli (strain K12) GN=cyoB PE=1 SV=1
MFGKLSLDAVPFHEPIVMVTIAGIILGGLALVGLITYFGKWTYLWKEWLTSVDHKRLGIM YIIVAIVMLLRGFADAIMMRSQQALASAGEAGFLPPHHYDQIFTAHGVIMIFFVAMPFVI GLMNLVVPLQIGARDVAFPFLNNLSFWFTVVGVILVNVSLGVGEFAQTGWLAYPPLSGIE YSPGVGVDYWIWSLQLSGIGTTLTGINFFVTILKMRAPGMTMFKMPVFTWASLCANVLII ASFPILTVTVALLTLDRYLGTHFFTNDMGGNMMMYINLIWAWGHPEVYILILPVFGVFSE IAATFSRKRLFGYTSLVWATVCITVLSFIVWLHHFFTMGAGANVNAFFGITTMIIAIPTG VKIFNWLFTMYQGRIVFHSAMLWTIGFIVTFSVGGMTGVLLAVPGADFVLHNSLFLIAHF HNVIIGGVVFGCFAGMTYWWPKAFGFKLNETWGKRAFWFWIIGFFVAFMPLYALGFMGMT RRLSQQIDPQFHTMLMIAASGAVLIALGILCLVIQMYVSIRDRDQNRDLTGDPWGGRTLE WATSSPPPFYNFAVVPHVHERDAFWEMKEKGEAYKKPDHYEEIHMPKNSGAGIVIAAFST IFGFAMIWHIWWLAIVGFAGMIITWIVKSFDEDVDYYVPVAEIEKLENQHFDEITKAGLK NGN
>sp|P0ABK2|CYDB_ECOLI Cytochrome d ubiquinol oxidase subunit 2 OS=Escherichia coli (strain K12) GN=cydB PE=1 SV=1
MIDYEVLRFIWWLLVGVLLIGFAVTDGFDMGVGMLTRFLGRNDTERRIMINSIAPHWDGN QVWLITAGGALFAAWPMVYAAAFSGFYVAMILVLASLFFRPVGFDYRSKIEETRWRNMWD WGIFIGSFVPPLVIGVAFGNLLQGVPFNVDEYLRLYYTGNFFQLLNPFGLLAGVVSVGMI ITQGATYLQMRTVGELHLRTRATAQVAALVTLVCFALAGVWVMYGIDGYVVKSTMDHYAA SNPLNKEVVREAGAWLVNFNNTPILWAIPALGVVLPLLTILTARMDKAAWAFVFSSLTLA CIILTAGIAMFPFVMPSSTMMNASLTMWDATSSQLTLNVMTWVAVVLVPIILLYTAWCYW KMFGRITKEDIERNTHSLY
>sp|Q6MIR4|NUOB_BDEBA NADH-quinone oxidoreductase subunit B OS=Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100) GN=nuoB PE=3 SV=1
MHNEQVQGLVSHDGMTGTQAVDDMSRGFAFTSKLDAIVAWGRKNSLWPMPYGTACCGIEF MSVMGPKYDLARFGAEVARFSPRQADLLVVAGTITEKMAPVIVRIYQQMLEPKYVLSMGA CASSGGFYRAYHVLQGVDKVIPVDVYIPGCPPTPEAVMDGIMALQRMIATNQPRPWKDNW KSPYEQA
>sp|Q89AU5|NUOB_BUCBP NADH-quinone oxidoreductase subunit B OS=Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp) GN=nuoB PE=3 SV=1
MKYTLTRVNISDDDQNYPREKKIQVSDPTKKYIQKNVFMGTLSKVLHNLVNWGRKNSLWP YNFGLSCCYVEMVTSFTSVHDISRFGSEVLRASPRQADFMVIAGTPFIKMVPIIQRLYDQ MLEPKWVISMGSCANSGGMYDIYSVVQGVDKFLPVDVYIPGCPPRPEAYIHGLMLLQKSI SKERRPLSWIIGEQGIYKANFNSEKKNLRKMRNLVKYSQDKN
>sp|Q82DY0|NUOB1_STRAW NADH-quinone oxidoreductase subunit B 1 OS=Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NCIMB 12804 / NRRL 8165 / MA-4680) GN=nuoB1 PE=3 SV=1
MGLEEKLPSGFLLTTVEQAAGWVRKASVFPATFGLACCAIEMMTTGAGRYDLARFGMEVF RGSPRQADLMIVAGRVSQKMAPVLRQVYDQMPNPKWVISMGVCASSGGMFNNYAIVQGVD HIVPVDIYLPGCPPRPEMLIDAILKLHQKIQSSKLGVNAEEAAREAEEAALKALPTIEMK GLLR


Astonishingly, certain bacteria that "everyone knows" are anaerobic turned up as aerobic when checked with the above Blast-query. (For example: Bacteroides fragilis, Desulfovibrio gigas, Moorella thermoacetica, and others.) It seems quite a number of so-called anaerobes have non-copper (heme only) cytochrome oxidases. (See this paper for further discussion.)

In any event, my Blast search turned up 1,089 positives (putative aerobes, some facultatively anaerobic) out of 1,373 bacterial species. I tagged the non-positives as anaerobes.

Of the 284 putative anaerobes, 87 scored positive in a Blast protein search (t-blast-n) for catalase. I used the following catalase sequences in my query: 


>sp|B0C4G1|KATG_ACAM1 Catalase-peroxidase OS=Acaryochloris marina (strain MBIC 11017) GN=katG PE=3 SV=1
MSSASKCPFSGGALKFTAGSGTANRDWWPNQLNLQILRQHSPKSNPMDKAFNYAEAFKSL DLADVKQDIFDLMKSSQDWWPADYGHYGPLFIRMAWHSAGTYRIGDGRGGAGTGNQRFAP INSWPDNANLDKARMLLWPIKQKYGAKISWADLMILAGNCALESMGFKTFGFAGGREDIW EPEEDIYWGAETEWLGDQRYTGDRDLEATLGAVQMGLIYVNPEGPNGHPDPVASGRDIRE TFGRMAMNDEETVALTAGGHTFGKCHGAGDDAHVGPEPEGARIEDQCLGWKSSFGTGKGV HAITSGIEGAWTTNPTQWDNNYFENLFGYEWELTKSPAGANQWVPQGGAGANTVPDAHDP SRRHAPIMTTADMAMRMDPIYSPISRRFLDNPDQFADAFARAWFKLTHRDMGPRSRYLGP EVPEEELIWQDPVPAVNHELINEQDIATLKSQILATNLTVSQLVSTAWASAVTYRNSDKR GGANGARIRLAPQRDWEVNQPAQLATVLQTLEAVQTTFNHSQIGGKRVSLADLIVLGGCA GVEQAAKNAGWYDVKVPFKPGRTDATQAQTDVTSFAVLEPRADGFRNYLKGHYPVSAEEL LVDKAQLLTLTAPEMTVLVGGLRVLNANVGQAQHGVFTHRPESLTNDFFLNLLDMSVTWA ATSEAEEVFEGRDRKTGALKWTGTRVDLIFGSNSQLRALAEVYGCEDSQQRFVQDFVAAW DKVMNLDRFDLA
>tr|D9RGS2|D9RGS2_STAAJ Catalase OS=Staphylococcus aureus (strain JKD6159) GN=katE PE=3 SV=1
MSQQDKKLTGVFGHPVSDRENSMTAGPRGPLLMQDIYFLEQMSQFDREVIPERRMHAKGS GAFGTFTVTKDITKYTNAKIFSEIGKQTEMFARFSTVAGERGAADAERDIRGFALKFYTE EGNWDLVGNNTPVFFFRDPKLFVSLNRAVKRDPRTNMRDAQNNWDFWTGLPEALHQVTIL MSDRGIPKDLRHMHGFGSHTYSMYNDSGERVWVKFHFRTQQGIENLTDEEAAEIIASDRD SSQRDLFEAIEKGDYPKWTMYIQVMTEEQAKSHKDNPFDLTKVWYHDEYPLIEVGEFELN RNPDNYFMDVEQAAFAPTNIIPGLDFSPDKMLQGRLFSYGDAQRYRLGVNHWQIPVNQPK GVGIENICPFSRDGQMRVVDNNQGGGTHYYPNNHGKFDSQPEYKKPPFPTDGYGYEYNQR QDDDNYFEQPGKLFRLQSEDAKERIFTNTANAMEGVTDDVKRRHIRHCYKADPEYGKGVA KALGIDINSIDLETENDETYENFEK
>sp|P60355|MCAT_LACPN Manganese catalase OS=Lactobacillus plantarum PE=1 SV=1
MFKHTRKLQYNAKPDRSDPIMARRLQESLGGQWGETTGMMSYLSQGWASTGAEKYKDLLL DTGTEEMAHVEMISTMIGYLLEDAPFGPEDLKRDPSLATTMAGMDPEHSLVHGLNASLNN PNGAAWNAGYVTSSGNLVADMRFNVVRESEARLQVSRLYSMTEDEGVRDMLKFLLARETQ HQLQFMKAQEELEEKYGIIVPGDMKEIEHSEFSHVLMNFSDGDGSKAFEGQVAKDGEKFT YQENPEAMGGIPHIKPGDPRLHNHQG
>sp|P42321|CATA_PROMI Catalase OS=Proteus mirabilis GN=katA PE=1 SV=1
MEKKKLTTAAGAPVVDNNNVITAGPRGPMLLQDVWFLEKLAHFDREVIPERRMHAKGSGA FGTFTVTHDITKYTRAKIFSEVGKKTEMFARFSTVAGERGAADAERDIRGFALKFYTEEG NWDMVGNNTPVFYLRDPLKFPDLNHIVKRDPRTNMRNMAYKWDFFSHLPESLHQLTIDMS DRGLPLSYRFVHGFGSHTYSFINKDNERFWVKFHFRCQQGIKNLMDDEAEALVGKDRESS QRDLFEAIERGDYPRWKLQIQIMPEKEASTVPYNPFDLTKVWPHADYPLMDVGYFELNRN PDNYFSDVEQAAFSPANIVPGISFSPDKMLQGRLFSYGDAHRYRLGVNHHQIPVNAPKCP FHNYHRDGAMRVDGNSGNGITYEPNSGGVFQEQPDFKEPPLSIEGAADHWNHREDEDYFS QPRALYELLSDDEHQRMFARIAGELSQASKETQQRQIDLFTKVHPEYGAGVEKAIKVLEG KDAK
>sp|Q9Z598|CATA_STRCO Catalase OS=Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) GN=katA PE=3 SV=1
MSQRVLTTESGAPVADNQNSASAGIGGPLLIQDQHLIEKLARFNRERIPERVVHARGSGA YGHFEVTDDVSGFTHADFLNTVGKRTEVFLRFSTVADSLGGADAVRDPRGFALKFYTEEG NYDLVGNNTPVFFIKDPIKFPDFIHSQKRDPFTGRQEPDNVFDFWAHSPEATHQITWLMG DRGIPASYRHMDGFGSHTYQWTNARGESFFVKYHFKTDQGIRCLTADEAAKLAGEDPTSH QTDLVQAIERGVYPSWTLHVQLMPVAEAANYRFNPFDVTKVWPHADYPLKRVGRLVLDRN PDNVFAEVEQAAFSPNNFVPGIGPSPDKMLQGRLFAYADAHRYRLGVNHTQLAVNAPKAV PGGAANYGRDGLMAANPQGRYAKNYEPNSYDGPAETGTPLAAPLAVSGHTGTHEAPLHTK DDHFVQAGALYRLMSEDEKQRLVANLAGGLSQVSRNDVVEKNLAHFHAADPEYGKRVEEA VRALRED
>Haloarcula marismortui strain ATCC 43049(v1, unmasked), Name: YP_136584.1, katG1, rrnAC2018, Type: CDS, Feature Location: (Chr: I, complement(1808213..1810405)) Genomic Location: 1808213-1810405
MLKTVLMPSPSKCSLMAKRDQDWSPNQLRLDILDQNARDADPRGTGFDYAEEFQELDLDAVKADLEELMTSSQDWWPADYGHYGPLFIRMAWHSAGTYRTTDGRGGASGGRQRFAPLNSWPDNANLDKARRLLWPIKKKYGRKLSWADLIVLAGNHAIESMGLKTFGWAGGREDAFEPDEAVDWGPEDEMEAHQSERRTDDGELKEPLGAAVMGLIYVDPEGPNGNPDPLASAENIRESFGRMAMNDEETAALIAGGHTFGKVHGADDPEENLGDVPEDAPIEQMGLGWENDYGSGKAGDTITSGIEGPWTQAPIEWDNGYIDNLLDYEWEPEKGPGGAWQWTPTDEALANTVPDAHDPSEKQTPMMLTTDIALKRDPDYREVMERFQENPMEFGINFARAWYKLIHRDMGPPERFLGPDAPDEEMIWQDPVPDVDHDLIGDEEVAELKTDILETDLTVSQLVKTAWASASTYRDSDKRGGANGARIRLEPQKNWEVNEPAQLETVLATLEEIQAEFNSARTDDTRVSLADLIVLGGNAAVEQAAADAGYDVTVPFEPGRTDATPEQTDVDSFEALKPRADGFRNYARDDVDVPAEELLVDRADLLDLTPEEMTVLVGGLRSLGATYQDSDLGVFTDEPGTLTNDFFEVVLGMDTEWEPVSESKDVFEGYDRETGEQTWAASRVDLIFGSHSRLRAIAEVYGADGAEAELVDDFVDAWHKVMRLDRFDLE
>sp|B2TJE9|KATG_CLOBB Catalase-peroxidase OS=Clostridium botulinum (strain Eklund 17B / Type B) GN=katG PE=3 SV=1
MTENKCPVTGKMGKATAGSGTTNKDWWPNQLNLNILHQNSQLSNPMSKDFNYAEEFKKLD FQALKVDLYMLMTDSQIWWPADYGNYGPLFIRMAWHSAGTYRVGDGRGGGSLGLQRFAPL NSWPDNINLDKARRLLWPIKKKYGNKISWADLLILTGNCALESMGLKTLGFGGGRVDVWE PQEDIYWGSEKEWLGDEREKGDKELENPLAAVQMGLIYVNPEGPNGNPDPLGSAHDVRET FARMAMNDEETVALIAGGHTFGKCHGAASPSYVGPAPEAAPIEEQGLGWKNTYGSGNGDD TIGSGLEGAWKANPTKWTMGYLKTLFKYDWELVKSPAGAYQWLAKNVDEEDMVIDAEDST KKHRPMMTTADLGLRYDPIYEPIARNYLKNPEKFAHDFASAWFKLTHRDMGPISRYLGPE VPKESFIWQDPIPLVKHKLITKKDITHIKKKILDSGLSISDLVATAWASASTFRGSDKRG GANGGRIRLEPQKNWEVNEPKKLNNVLNTLKQIKENFNSSHSKDKKVSLADIIILGGCVG IEQAAKRAGYNINVPFIPGRTDAIQEQTDVKSFAVLEPKEDGFRNYLKTKYVVKPEDMLI DRAQLLTLTAPEMTVLIGGMRVLNCNYNKSKDGVFTNRPECLTNDFFVNLLDMNTVWKPK SEDKDRFEGFDRETGELKWTATRVDLIFGSNSQLRAIAEVYACDDNKEKFIQDFIFAWNK IMNADRFEIK
>sp|Q59635|CATB_PSEAE Catalase OS=Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) GN=katB PE=3 SV=1
MNPSLNAFRPGRLLVAASLTASLLSLSVQAATLTRDNGAPVGDNQNSQTAGPNGSVLLQD VQLLQKLQRFDRERIPERVVHARGTGAHGEFVASADISDLSMAKVFRKGEKTPVFVRFSA VVHGNHSPETLRDPRGFATKFYTADGNWDLVGNNFPTFFIRDAIKFPDMVHAFKPDPRSN LDDDSRRFDFFSHVPEATRTLTLLYSNEGTPASYREMDGNSVHAYKLVNARGEVHYVKFH WKSLQGQKNLDPKQVAEVQGRDYSHMTNDLVSAIRKGDFPKWDLYIQVLKPEDLAKFDFD PLDATKIWPGIPERKIGQMVLNRNVDNFFQETEQVAMAPSNLVPGIEPSEDRLLQGRLFA YADTQMYRVGANGLGLPVNRPRSEVNTVNQDGALNAGHSTSGVNYQPSRLDPREEQASAR YVRTPLSGTTQQAKIQREQNFKQTGELFRSYGKKDQADLIASLGGALAITDDESKYIMLS YFYKADSDYGTGLAKVAGADLQRVRQLAAKLQD

The first of these is a cyanobacterial katG (large subunit) type of catalase, perhaps representative of primitive protobacterial catalase. The second sequence in the above list is classic Staphylococcus catalase (katE). The third is a manganese-containing catalase from Lactobacillus. (This brought the most hits, by the way.) The others are, in turn, katA catalase from Proteus and Streptomyces, two organisms that are far apart in genomic G+C content (and rather distant phylogenetically); an Archaeal catalase (even though none of the 1,373 species in my organism list was Archaeal in origin; but you never know whether a given bacterium may have obtained its catalase through horizontal gene transfer); then a known-valid anaerobic catalase from Clostridium botulinum, and finally a Pseudomonas katB catalase. The idea was to cover as much ground, phylogenetically and enzymatically, as possible, with big and small-subunit catalases, of the heme as well as the manganese variety, from aerobic and anaerobic bacteria of high and low genomic G+C content, as well as an archaeal catalase for good measure.

Here, then, finally, is the list of 87 catalase-positive strict anaerobes:

Acetohalobium arabaticum strain DSM 5501
Alkaliphilus metalliredigens strain QYMF
Alkaliphilus oremlandii strain OhILAs
Anaerococcus prevotii strain ACS-065-V-Col13
Anaerococcus vaginalis strain ATCC 51170
Anaerofustis stercorihominis strain DSM 17244
Anaerostipes caccae strain DSM 14662
Anaerostipes sp. strain 3_2_56FAA
Anaerotruncus colihominis strain DSM 17241
Bacteroides capillosus strain ATCC 29799
Bacteroides pectinophilus strain ATCC 43243
Brachyspira hyodysenteriae strain ATCC 49526; WA1
Brachyspira intermedia strain PWS/A
Brachyspira pilosicoli strain 95/1000
Candidatus Arthromitus sp. SFB-mouse-Japan
Carnobacterium sp. strain 17-4
Clostridium acetobutylicum strain ATCC 824
Clostridium asparagiforme strain DSM 15981
Clostridium bartlettii strain DSM 16795
Clostridium bolteae strain ATCC BAA-613
Clostridium botulinum A2 strain Kyoto
Clostridium butyricum strain 5521
Clostridium cellulovorans strain 743B
Clostridium cf. saccharolyticum strain K10
Clostridium citroniae strain WAL-17108
Clostridium clostridioforme strain 2_1_49FAA
Clostridium difficile QCD-37x79
Clostridium hathewayi strain WAL-18680
Clostridium hylemonae strain DSM 15053
Clostridium kluyveri strain DSM 555
Clostridium lentocellum strain DSM 5427
Clostridium leptum strain DSM 753
Clostridium ljungdahlii strain ATCC 49587
Clostridium novyi strain NT
Clostridium ramosum strain DSM 1402
Clostridium saccharolyticum strain WM1
Clostridium scindens strain ATCC 35704
Clostridium spiroforme strain DSM 1552
Clostridium sporogenes strain ATCC 15579
Clostridium tetani strain Massachusetts substrain E88
Coprobacillus sp. strain 3_3_56FAA
Coprococcus comes strain ATCC 27758
Coprococcus sp. strain ART55/1
Dethiobacter alkaliphilus strain AHT 1
Dorea formicigenerans strain 4_6_53AFAA
Dorea longicatena strain DSM 13814
Erysipelotrichaceae bacterium strain 21_3
Eubacterium dolichum strain DSM 3991
Eubacterium eligens strain ATCC 27750
Eubacterium siraeum strain 70/3
Eubacterium ventriosum strain ATCC 27560
Flavonifractor plautii strain ATCC 29863
Halothermothrix orenii strain DSM 9562; H 168
Holdemania filiformis strain DSM 12042
Lachnospiraceae bacterium strain 1_1_57FAA
Lactobacillus curvatus strain CRL 705
Lactobacillus sakei subsp. sakei strain 23K
Mahella australiensis strain 50-1 BON
Natranaerobius thermophilus strain JW/NM-WN-LF
Oscillibacter valericigenes strain Sjm18-20
Parabacteroides distasonis strain ATCC 8503
Parabacteroides johnsonii strain DSM 18315
Parabacteroides sp. strain D13
Pediococcus acidilactici strain DSM 20284
Pediococcus pentosaceus strain ATCC 25745
Pelotomaculum thermopropionicum strain SI
Pseudoflavonifractor capillosus strain ATCC 29799
Pseudoramibacter alactolyticus strain ATCC 23263
Roseburia hominis strain A2-183
Roseburia intestinalis strain M50/1
Ruminococcaceae bacterium strain D16
Ruminococcus bromii strain L2-63
Ruminococcus obeum strain A2-162
Ruminococcus sp. strain 18P13
Ruminococcus torques strain L2-14
Sphaerochaeta pleomorpha strain Grapes
Spirochaeta coccoides strain DSM 17374
Spirochaeta sp. strain Buddy
Subdoligranulum sp. strain 4_3_54A2FAA
Tepidanaerobacter sp. strain Re1
Thermoanaerobacter brockii subsp. finnii strain Ako-1
Thermoanaerobacter ethanolicus strain CCSD1
Thermoanaerobacter pseudethanolicus strain 39E; ATCC 33223
Thermoanaerobacter sp. strain X514
Thermosediminibacter oceani strain DSM 16646
Treponema brennaborense strain DSM 12168
Turicibacter sanguinis strain PC909

Note that these are all bacteria; no archaeons are included. (And yes, there are catalase-positive anaerobes among the Archaea.) The reason you don't see Bacteroides fragilis (which is catalase-positive) on the list is that, as explained before, B. fragilis ended up being classified an aerobe by my cytochrome-oxidase-based initial search. Even though "everybody knows" B. fragilis is anaerobic.

Incidentally, Blast searches were done with an E-value cutoff of 1e-5, to reduce the chance of false positives. (E-value is a measure of how likely it is that a given Blast match could have occurred due to chance. A threshold value of 1e-5 means the only matches that will be accepted are those that have less than a 1-in-100,000 chance of occurring by chance.)

If you learn of any other catalase-positive anaerobes that should be on this list, do be sure to let me know!

A Catalase Conundrum

When I was in grad school (U.C. Davis) in the late 1970s, the bacterial world was simply the prokaryotic world, and vice versa. There hadn't yet come a distinction between eubacteria and Archaea. But now we know, or think we know, that prokaryota come in two fundamental flavors: the true bacteria (eubacteria), and the Archaea (primitive extremophiles). If you were to want to count organelles (mitochondria, chloroplasts, others) as a third fundamental grouping, I suppose you could, with some justification.

At this writing, about 400 distinct Archaeal isolates, belonging to around 75 genera, have been DNA-sequenced. You can see a list of them by going to http://genomevolution.org/CoGe/OrganismView.pl?org_desc=Archaea and looking in the Organisms box. You'll see over 200 organisms listed, but bear in mind they belong to only about 75 genera. (Most genera are represented by more than one species and/or more than one isolate per species, in other words.)

Salt-loving Archaea species have been found growing in borax-saturated
desert ponds. The species growing in this small lake produce a
carotenoid pigment that gives the water a pink appearance.

The Archaea were once thought to be exclusively anaerobes, but it turns out there are a couple dozen aerobic (or facultatively anaerobic) genera in the group. In my own spare-time research, I've found that about 20% of the 75 sequenced Archaeons (all of them obligate anaerobes) have a catalase gene. (Catalase is the enzyme that breaks hydrogen peroxide down to water and oxygen.) Oddly, very few of the aerobic Archaea (except for the Halobacteriaceae group) show any evidence of having catalase. This is exactly the reverse of what's expected. In the rest of the living kingdom (from bacteria to higher plants and animals), aerobes universally have catalase; strict anaerobes don't have catalase (or at least, they aren't supposed to; but see this post for some surprising exceptions).

This is a hugely unexpected finding: Many anaerobic Archaeons have catalase, but not all aerobic ones do. Some enterprising grad student should tackle this and make a thesis project out of it.

In case you're that student, here are some additional clues.

Let's back up for a second and look at the Big Picture. No matter where on the Tree of Life you go, catalases come in only a few major types. (See the excellent 2003 review paper by Chelikani, Fita, and Loewen for details.) For example, there are heme-containing and non-heme catalases. Most of the time, what we think of as "catalase" is heme-containing catalase (and yes, that means it contains iron). In the heme-containing group, you have monofunctional catalase as well as bifunctional catalase-peroxidases or hydroperoxidases (katG). The monofunctionals come in big- and small-subunit varieties. (The biggies have subunits of 75 kDa or more and comprise just over 2100 base-pairs of DNA. The smalls have subunits under 60 kDa and typically top out at 1500 base-pairs.)

Here's what you really need to know: Within the monofunctionals, there are three clades (major subgroupings) of catalase. Clades 1 and 3 are small-subunit enzymes. Clade 1 is primarily of plant origin and is relatively rare in bacteria (the best-known examples probably being katX of Bacillus subtilis and catF of Pseudomonas syringae). Clade 3 takes in a huge number of catalases from bacteria, fungi, and various eukaryotes. (For Clade 3, think Staphylococcus catalase.)  Clade 2 is the large-subunit enzyme (think E. coli katE catalase).

The multifunctionals tend to be large (over 2100 base-pairs of DNA).

The non-heme catalases contain manganese instead of iron and are not your typical catalases. Let's leave it at that.

What do the Archaeons produce? From what little probing I've done, it seems the anaerobic Archaeons that have catalase use a modified Clade 3 type of enzyme that has little in common with other Clade 3 catalases. A few of the methane producers show good sequence agreement with Bacteroides fragilis catalase, but most anaerobic Archaeal catalases do not show good sequence concordance with any known eubacterial catalases. So it's entirely possible that a fourth clade of purely Archaeal small-subunit catalases (unlike anything else in the plant or animal worlds) awaits characterization.

The aerobic Archaeons that have catalase are all halophiles (members of the Halobacteriaceae), and all have large-subunit multifunctional peroxidases similar to those of the Cyanobacteria.

Mysteries waiting to be solved:

• Why is it the aerobes Sulfolobus, Pyrobaculum, and Aeropyrum do not appear to have catalase? Is it that they don't have catalase, or do they have some as-yet-undiscovered new type of catalase?
• Why is it that certain methane-generating anaerobes (e.g., Methanosarcina) have Clade 3 catalases but the rest of the methane-producing Archaea have catalases that don't match anything else in the living world? Did the former group get their catalase(s) by way of horizontal gene transfer from anaerobic eubacteria?
• Did the multifunctional catalases of the Halobacteriaceae originally come from cyanobacteria (perhaps by way of plasmids)?
• What overlap, if any, exists between Archaeal catalases and the catalases of algal chloroplasts?

If you find the answers to any of these, let me know!

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.