Tuesday, November 10, 2015

A cyanobacterium with an anoxygenic Type II reaction center from purple bacteria? (Contamination)

With the surge of genome sequences it is crazy what you can find. As I was doing a few BLASTs searching for new photosynthetic reaction center proteins in the database I noticed that the genome of Lyngbya confervoides BDU141951, which was reported early this year (link), contained genes that encode an anoxygenic Type II reaction center from Alphaproteobacteria (Purple Bacteria).

The three genes for the L, M and H subunit.

NameAccessionStartStopStrandGeneIDLocusLocus tagProtein productLengthProtein name
UnNZ_JTHE01000129.114472301+--QQ91_RS05655WP_039723522.1284photosynthetic reaction center subunit L
UnNZ_JTHE01000129.123153298+--QQ91_RS05660WP_039723523.1327photosynthetic reaction center subunit M
UnNZ_JTHE01000254.130083799---QQ91_RS10590WP_039724487.1263photosynthetic reaction center subunit H



1. The best hit for the L subunit was to:

Photosynthetic reaction center subunit L [Oceanibaculum indicum]
ref|WP_008944428.1|

ScoreExpectMethodIdentitiesPositivesGaps
442 bits(1137) 2e-153 Compositional matrix adjust. 222/280(79%) 240/280(85%) 1/280(0%)


2. The best hit for the M subunit was to:

Photosynthetic reaction center subunit M [Ahrensia sp. R2A130]
ref|WP_009758337.1|


ScoreExpectMethodIdentitiesPositivesGaps
457 bits(1175) 5e-158 Compositional matrix adjust. 221/308(72%) 260/308(84%) 2/308(0%)


3. The best hit for the H subunit was to:

Photosynthetic reaction centre, H-chain [Hoeflea phototrophica]
ref|WP_007196606.1|

ScoreExpectMethodIdentitiesPositivesGaps
282 bits(721) 5e-91 Compositional matrix adjust. 139/258(54%) 175/258(67%) 2/258(0%)

What is going on?

When I BLASTed the BchZ subunit of chlorophyllide a reductase from Rhodobacter sphaeroides, which makes bacteriochlorophyllide a from chlorophyllide a... the best hit was to this same strain of cyanobacteria: but it seems it is a fragment only (see image below, never mind the annotation). A close homologous to BchY did not retrieve anything out of the ordinary, the same for BchX. So this cyanobacterium cannot really make bacteriochlorophyll... I wonder if the anoxygenic Type II reaction center in this strain could be active using chlorophyll a along side PSII and PSI.

The fact that the best hits to the reaction center proteins are below 80% means that the alphaproteobacterium that donated this genes represents at least a new genus or something.


UPDATE: It turned out after all to be contamination. It might be that the cultures used were not completely axenic. It's a pity.

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