Category:LBGA: Difference between revisions
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Archaeal lipid is composed of sn-glycerol 1-phosphate and ether-linked isoprenoids. This composition is different from lipid in eubacteria and eukaryotes, which comprises of sn-glycerol 3-phosphate and ester-linked fatty acids. Responsible biosynthetic enzymes are also non-homologous. Archaea also contains tetraether lipids in which two isoprenes are ether-linked with two glycerols at both ends (caldarchaeol).
Archaeal lipid is composed of ''sn''-glycerol 1-phosphate and ether-linked isoprenoids (C20 phytanes). This composition is different from lipids in eubacteria and eukaryotes, which comprise of sn-glycerol 3-phosphate and ester-linked fatty acids. Responsible biosynthetic enzymes are also non-homologous. Archaea also contains tetraether lipids in which two isoprenes (C40 biphytanes) are ether-linked with two glycerols at both ends (caldarchaeol).
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アーキア<ref>古細菌と呼ばれることが多いのですが、真性細菌と明確に区別するためにここではアーキアと記します。</ref>の脂質は、
アーキア<ref>古細菌と呼ばれることが多いのですが、真正細菌と明確に区別するためにここではアーキアと記します。</ref>の脂質は、
sn-グリセロール1リン酸にメバロン酸由来のイソプレン骨格がエーテル結合しています。
''sn''-グリセロール1リン酸にメバロン酸由来のイソプレン骨格（C20フィタン）がエーテル結合しています (snがわからない人は[http://metabolomics.jp/wiki/Aritalab:Lecture/Biochem/Isomer 異性体]のページを参照してください)。
これは、グリセロール3リン酸と脂肪酸を利用する真性細菌や真核生物と全く異なる構造で、生合成をおこなう酵素も相同ではありません。またテトラエーテル型と呼ばれるイソプレン骨格が末端で2分子のグリセロールとエーテル結合した環状脂質（カルドアーキオール）も広く存在します。
これは、グリセロール3リン酸と脂肪酸を利用する真正細菌や真核生物と全く異なる構造で、生合成をおこなう酵素も相同ではありません。またテトラエーテル型と呼ばれる、長さ40のバイフィタンが末端で2分子のグリセロールとエーテル結合した環状脂質（カルドアーキオール）も広く存在します。
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==={{Bilingual|系統|Phylogeny}}===
==={{Bilingual|系統|Phylogeny}}===
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Archaea are separated into two major phyla (Crenarchaeota and Euryarchaeota)<ref>Studies on mostly uncultured archaea identified other small phyla such as Korarchaeota (Barns et al. 1996 PMID 8799176), Nanoarchaeota (Huber et al. 2002 PMID 11986665), and the Thaumarchaeota (Brochier-Armanet et al. 2002 PMID 18274537). They are characterized only by genome sequences and not considered here.</ref> and ecologically three different characters exist (Table 1). Genus names are summarized [[Index:LBGA|here]].
Archaea are separated into two major phyla (Crenarchaeota and Euryarchaeota)<ref>Studies on mostly uncultured archaea identified other small phyla such as Korarchaeota (Barns et al. 1996 PMID 8799176), Nanoarchaeota (Huber et al. 2002 PMID 11986665), and the Thaumarchaeota (Brochier-Armanet et al. 2002 PMID 18274537). They are characterized only by genome sequences and not considered here.</ref> and three ecologically different microbes exist: thermophile, halophile, and methanogen (Table 1). Previously archaea were believed to exist only in extreme environments, but their habitat is actually ubiquitous from sea surface to deep underground. Genus names are summarized [[Index:LBGA|here]].
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アーキアは大きくCrenarchaeotaとEuryarchaetaという二大グループに分かれ<ref>難培養性のアーキアとしてKorarchaeota (Barns et al. 1996 PMID 8799176), Nanoarchaeota (Huber et al. 2002 PMID 11986665), Thaumarchaeota (Brochier-Armanet et al. 2002 PMID 18274537)などの小グループも見つかっていますがゲノム解析のみなのでここでは省略します。</ref>、
アーキアは大きくCrenarchaeotaとEuryarchaetaという二大グループに分かれ<ref>難培養性のアーキアとしてKorarchaeota (Barns et al. 1996 PMID 8799176), Nanoarchaeota (Huber et al. 2002 PMID 11986665), Thaumarchaeota (Brochier-Armanet et al. 2002 PMID 18274537)などの小グループも見つかっていますが難培養性でゲノム解析のみのため、生物分類上は確定していません。</ref>、
三通りの特徴を持ちます（表1）。属名一覧は[[Index:LBGA|別ページ]]にまとめています。
アンモニア酸化菌、好熱菌、好塩菌、メタン生成菌の４種類が含まれます（表1）。以前は極限環境に住むと考えられていましたが、特にアンモニア酸化菌 (thaumarchaeota) は海から地底まで遍在することがわかっています。属名一覧は[[Index:LBGA|別ページ]]にまとめています。
}}
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|-
|-
!  Phyrum (綱) || Order (目) || Family (科) || {{Bilingual|特徴|Character}} || {{Bilingual|グラム染色|Gram-staining}}
!  Phyrum (綱) || Order (目) || Family (科) || {{Bilingual|特徴|Character}} || {{Bilingual|グラム染色|Gram-staining}}
|- style="background-color:#fd3"
!rowspan="1"|thaumarchaeota
|cenarchaeales || cenarchaeaceae
|{{Bilingual|アンモニア酸化菌|ammonia oxidizer}} || ? (unculturable)
|- style="background-color:#fdd"
|- style="background-color:#fdd"
!rowspan="3"|crenarchaeota  
!rowspan="3"|crenarchaeota  
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==={{Bilingual|脂質命名法|Nomenclature}}===
==={{Bilingual|脂質命名法|Nomenclature}}===
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Much of archaeal lipid were named by a Japanese research group<ref>Nishihara M, Morii H, Koga Y (1987) Structure determination of a quartet of novel tetraether lipids from Methanobacterium thermoautotrophicum. ''J Biochem'' 101:1007-1015 PMID 3611039</ref>. Note that sn-1 position of glycerol is open in the pictures below.
Much of archaeal lipid were named by a Japanese research group<ref>Nishihara M, Morii H, Koga Y (1987) Structure determination of a quartet of novel tetraether lipids from Methanobacterium thermoautotrophicum. ''J Biochem'' 101:1007-1015 PMID 3611039</ref>. Note that sn-1 position of glycerol is at the bottom of the pictures and the ether bond at the sn-2 position is below the paper plane.
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アーキア脂質の名称の多くは日本人によって名付けられました。以下の図ではグリセロールの sn-1 位が -OH として表示されています。通常のグリセロ脂質の描き方とは向きが異なるので注意してください。
アーキア脂質の名称の多くは日本人によって名付けられました。以下の図ではグリセロールの sn-1 位が 下側で-OH として表示されています。sn-2 位の水酸基は紙面の奥側です。通常のグリセロ脂質の描き方とは向きが異なるので注意してください。
}}
}}
{|  
{|  
|-
|-
!Archaeol (= 2,3-di-O-alkyl sn-glycerol diether) [[Image:LBGAA.png]]
!Archaeol (= 2,3-di-O-alkyl sn-glycerol diether) <small>[[Image:LBGAA.png|link=Category:LBGAA]]<br/>[[LBGAAB0N01|C20/20]], [[LBGAAB0N02|C25/20]], [[LBGAAB0N03|C25/25]]</small>
|{{Twocolumn
|{{Twocolumn
|The alkyl chain is either C20- or C25-isoprene. Archaetidic acid refers to its monophophate ether.
|The alkyl chain is C20-isoprane ([[Reference:Sehgal SN:Kates M:Gibbons NE:,Can. J. Biochem. Physiol.,1962,40,69|Sehgal et al 1962]] <ref>Few species contain C25/25 or C20/25 isopranoids.</ref>). Archaetidic acid refers to its monophophate ether.
|アルキル基はC20かC25のイソプレン。Archaetidic acid はその1リン酸エステルです。
|アルキル基はC20のイソプラン（飽和イソプレン）。Archaetidic acid はその1リン酸エステルです。
}}
}}
|-
|-
!Caldarchaeol [[Image:LBGAC.png]]
!Caldarchaeol [[Image:LBGAC.png|link=Category:LBGAC]]
|{{Twocolumn
|{{Twocolumn
|An tetraether where 2 glycerol molecules are connected with 2 alkanediols at sn-2 and sn-3 positions. It was first identified from a hyperthermophil, and therefore has "cald" (i.e. hot) in its name.
|An tetraether where 2 glycerol molecules are connected with 2 alkanediols at sn-2 and sn-3 positions. [[Reference:Langworthy_TA:,Biochim._Biophys._Acta,1977,487,37|Langworthy]] found the structure from ''Thermoplasma acidophilum'' in 1977. Its name "cald" (i.e. hot) originates its discovery from a hyperthermophil.
|2分子のグリセロールがsn-2, sn-3 位でアルカンジオールとエーテル結合したテトラエーテル。超高熱菌から見出されたため cald (ラテン語で「熱い」) の名前がつきます。
|2分子のグリセロールがsn-2, sn-3 位でアルカンジオールとエーテル結合したテトラエーテル。Langworthy が ''Thermoplasma acidophilum'' より発見し、超高熱菌から見出されたため cald (ラテン語で「熱い」) の名前がつきます。
}}
}}
|-
|-
!Isocaldarchaeol [[Image:LBGAI.png]]
! Calditocaldarchaeol [[Image:LBGAD.png|link=Category:LBGAD]]
|{{Twocolumn
|{{Twocolumn
|A geometric isomer of caldarchaeol where the alkanediols connect sn-2 and sn-2 (or sn-3 and sn-3) positions. Gr&auml;ther et al. first found this regioisomer in ''Methanothermobacter marburgensis'' <ref>Graether O, Arigoni D (1995) Detection of regioisomeric macrocyclic tetraethers in the lipids of Methanobacterium thermoautotrophicum and other archaeal organisms. ''J Chem Soc Chem Commun'' 1995, 405 [http://dx.doi.org/10.1039/C39950000405 DOI]</ref>. It was also found in ''Thermoplasma acidophilum'' and ''Sulfolobus solfataricus''.
|Calditol refers to a 5-carbon cyclic polyol [ 2-hydroxymethyl 1-(dihydroxypropoxy) 2,3,4,5-cyclopentanetetraol ] , which is connected to sn-1 glycerol by an ether linkage. It was first identified from ''Caldariella acidophila'' (now ''Sulfolobus solfataricus'') and was called nonitol with a wrong structure. Bleriot et al., 2002).<ref>Bleriot Y, Untersteller E, Fritz B, Sinay P (2002) Total Synthesis of calditol: Structural clarification of this typical component of archaea order Sulfolobales. ''Chemistry'' 8(1):240-246 PMID 11822455</ref> shows its brief history.
|片方のグリセロールがCaldarchaeolと向きの違う異性体。最初 Gr&auml;ther らが''Methanothermobacter marburgensis''より見つけ、''Thermoplasma acidophilum'' や ''Sulfolobus solfataricus'' でも確認されました。
|カルジトールは水酸基を5つ有する炭素五員環で、sn-1部位でグリセロールにエーテル結合しています。当初 ''Caldariella acidophila'' MT-4 (現 ''Sulfolobus solfataricus'') に見出された際に異なる構造が報告され nonitol と呼ばれた時期もありました。下のBleriotらの論文に経緯があります。
}}
}}
|-
|-
! Calditocaldarchaeol [[Image:LBGAD.png]]
!(Macro)Cyclic Archaeol [[Image:LBGAY.png|link=https://lipidbank.jp/wiki/Volatile:ListMol?my_1=LBGAY]]
|{{Twocolumn
|{{Twocolumn
|Calditol refers to a 5-carbon cyclic polyol [ 2-hydroxymethyl 1-(dihydroxypropoxy) 2,3,4,5-cyclopentanetetraol ] , which is connected to sn-1 glycerol by an ether linkage. It was first identified from ''Caldariella acidophila'' (now ''Sulfolobus solfataricus'' A.T.C.C. 49155) and was called nonitol with a wrong structure. (A brief history is in Bleriot et al., 2002).<ref>Bleriot Y, Untersteller E, Fritz B, Sinay P (2002) Total Synthesis of calditol: Structural clarification of this typical component of archaea order Sulfolobales. ''Chemistry'' 8(1):240-246 PMID 11822455</ref>)
|(Macro)Cyclic archaeol is characteristic to thermophilic archaea such as ''M. jannaschii''.  It is believed to increase membrane rigidity under higher pressure. Its amount is reported to increase in cultures of high temperature or pressure. <ref>Sprott GD, Meloche M, Richards JC (1991) Proportions of diether, macrocyclic diether, and tetraether lipids in Methanococcus jannaschii grown at different temperatures. ''J Bacteriol'' 173, 3907-3910 PMID 2050642</ref><ref>Kaneshiro SM, Clark DS (1995) Pressure effects on the composition and thermal behavior of lipids from the deep-sea thermophile methanococcus jannaschii. ''J Bacteriol'' 177, 3668-3672 PMID 7601829</ref>
|カルジトールは水酸基を5つ有する炭素五員環で、sn-1部位でグリセロールにエーテル結合しています。当初 ''Caldariella acidophila'' MT-4 (現 ''Sulfolobus solfataricus'' A.T.C.C. 49155) に見出された際に異なる構造が報告され nonitol と呼ばれた時期もありました。下のBleriotらの論文に経緯があります。
|環状アーキオールは好熱菌 ''M. jannaschii'' にみられ、膜構造の強度を増すと考えられています。生育温度の上昇、または圧力の上昇で量が増えると報告されています。
}}
|-
!Cyclic Archaeol [[Image:LBGAY.png]]
|{{Twocolumn
|(Macro)Cyclic archaeol is characteristic to thermophilic archaea such as ''M. jannaschii''.  It is believed to increase membrane rigidity in higher pressures.
|環状アーキオールは ''M. jannaschii'' の生育温度を上げたり圧力を上げると量が増えることが知られています<ref>Sprott GD, Meloche M, Richards JC (1991) Proportions of diether, macrocyclic diether, and tetraether lipids in Methanococcus jannaschii grown at different temperatures. ''J Bacteriol'' 173, 3907-3910 PMID 2050642</ref><ref>Kaneshiro SM, Clark DS (1995) Pressure effects on the composition and thermal behavior of lipids from the deep-sea thermophile methanococcus jannaschii. ''J Bacteriol'' 177, 3668-3672 PMID 7601829</ref>
}}
}}
|}
|}
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<references/>
<references/>


=={{Bilingual|ID番号 (ページ名) の設計|Design of Fat acyl Page Titles}}==
=={{Bilingual|ID番号 (ページ名) の設計|Design of Page Titles}}==
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Archaeal lipid is categorized in glycerolipid (LBG). Each ID contains information on the core-lipid type, chemical modification of polar head, and attached sugars.
Archaeal lipid is categorized in glycerolipid (LBG). Each ID contains information on the core-lipid type, chemical modification of polar head, and attached sugars.
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! Core-lipid Structure
! Core-lipid Structure
|- valign="top"
|- valign="top"
|[[Volatile:ListMol?my_1=LBGAA|A: archaeol]] (C20,C20 type below) <br/>[[Image:LBGAA.png]]
|[[:Category:LBGAA|A: archaeol]] <br/>[[Image:LBGAA.png|link=Category:LBGAA]]
|-
|-
|[[Volatile:ListMol?my_1=LBGAH|H: hydroxy & methoxy archaeol]] (sn-2-hydroxy below) <br/>[[Image:LBGAH.png]]
|{{#volatile:ListMol|H: hydroxy archaeol|LBGAH}} <br/>[[Image:LBGAH.png|link=https://lipidbank.jp/wiki/Volatile:ListMol?my_1=LBGAH]]
|-
|-
|[[Volatile:ListMol?my_1=LBGAU|U: unsaturated (alkenyl) archaeol]]<br/>[[Image:LBGAU.png]]
|{{#volatile:ListMol|U: unsaturated (alkenyl) archaeol|LBGAU}}<br/>[[Image:LBGAU.png|link=https://lipidbank.jp/wiki/Volatile:ListMol?my_1=LBGAU]]
|-
|-
|[[Volatile:ListMol?my_1=LBGAC|C: caldarchaeol]] (tetraether type)<br/>[[Image:LBGAC.png]]
|[[:Category:LBGAC|C: caldarchaeol]] (tetraether type)<br/>[[Image:LBGAC.png|link=Category:LBGAC]]
|-
|-
|[[Volatile:ListMol?my_1=LBGAD|D: calditocaldarchaeol]]<br/>[[Image:LBGAD.png]]
|[[:Category:LBGAD|D: irregular caldarchaeol]] (e.g. calditocald- or crenarchaeol, trialkyl or H-shaped archaeol)<br/>[[Image:LBGAD.png|link=Category:LBGAD]]
|-
|-
|[[Volatile:ListMol?my_1=LBGAY|Y: cyclic archaeol]]<br/>[[Image:LBGAY.png]]
|{{#volatile:ListMol|Y: cyclic archaeol|LBGAY}}<br/>[[Image:LBGAY.png|link=https://lipidbank.jp/wiki/Volatile:ListMol?my_1=LBGAY]]
|}
|}


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{| class="wikitable" border="1" cellpadding="2" cellspacing="1" margin: 1em 1em 1em 1em"
{| class="wikitable" border="1" cellpadding="2" cellspacing="1" margin: 1em 1em 1em 1em"
! Polar-head Type
! Polar-head Type
|- valign="top"
|[[Volatile:ListMol?my_1=LBGA.N|N:]] glycans<br/>
|-
|[[Volatile:ListMol?my_1=LBGA.P|P:]] phosphate or alcohol (OH)<br/>[[Image:LBGAxP.png]]
|-
|[[Volatile:ListMol?my_1=LBGA.C|C:]] phosphocholine<br/>[[Image:LBGAxC.png]]
|-
|[[Volatile:ListMol?my_1=LBGA.E|E:]] phosphoethanolamine<br/>[[Image:LBGAxE.png]]
|-
|[[Volatile:ListMol?my_1=LBGA.I|I:]] phosphoinositol<br/>[[Image:LBGAxI.png]]
|-
|[[Volatile:ListMol?my_1=LBGA.S|S:]] phosphoserine<br/>[[Image:LBGAxS.png]]
|-
|[[Volatile:ListMol?my_1=LBGA.G|G:]] phosphoglycerol<br/>[[Image:LBGAxG.png]]
|-
|[[Volatile:ListMol?my_1=LBGA.A|A:]] aminopentanetetrol<br/>[[Image:LBGAxA.png]]
|-
|-
|[[Volatile:ListMol?my_1=LBGA.X|X:]] others
|{{#volatile:ListMol|B:|LBGA.B}} no group<br/>
|- valign="top"   
|{{#volatile:ListMol|N:|LBGA.N}} saccharides<br/>
|-                 
|{{#volatile:ListMol|P:|LBGA.P}} phosphate or alcohol<br/>[[Image:LBGAxP.png|60px|link=https://lipidbank.jp/wiki/Volatile:ListMol?my_1=LBGA.P]]
|-                 
|{{#volatile:ListMol|C:|LBGA.C}} phosphocholine<br/>[[Image:LBGAxC.png|100px|link=https://lipidbank.jp/wiki/Volatile:ListMol?my_1=LBGA.C]]
|-                 
|{{#volatile:ListMol|E:|LBGA.E}} phosphoethanolamine<br/>[[Image:LBGAxE.png|100px|link=https://lipidbank.jp/wiki/Volatile:ListMol?my_1=LBGA.E]]
|-                 
|{{#volatile:ListMol|I:|LBGA.I}} phosphoinositol<br/>[[Image:LBGAxI.png|95px|link=https://lipidbank.jp/wiki/Volatile:ListMol?my_1=LBGA.I]]
|-                 
|{{#volatile:ListMol|S:|LBGA.S}} phosphoserine<br/>[[Image:LBGAxS.png|100px|link=https://lipidbank.jp/wiki/Volatile:ListMol?my_1=LBGA.S]]
|-                 
|{{#volatile:ListMol|G:|LBGA.G}} phosphoglycerol<br/>[[Image:LBGAxG.png|115px|link=https://lipidbank.jp/wiki/Volatile:ListMol?my_1=LBGA.G]]
|-                 
|{{#volatile:ListMol|A:|LBGA.A}} aminopentanetetrol<br/>[[Image:LBGAxA.png|115px|link=https://lipidbank.jp/wiki/Volatile:ListMol?my_1=LBGA.A]]
|-                 
|{{#volatile:ListMol|X:|LBGA.X}} others
|}
|}


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! Sugar Type
! Sugar Type
|- valign="top"
|- valign="top"
|[[Volatile:ListMol?my_1=LBGA...N|N:]] inositol only or no sugar
|{{#volatile:ListMol|N:|LBGA...N}} inositol only or no sugar
|-
|-                
|[[Volatile:ListMol?my_1=LBGA...G|G:]] glucose and galactose<br/>[[Image:LBGAxx1Glc.png]]<br/>[[Image:LBGAxx1Gal.png]]
|{{#volatile:ListMol|G:|LBGA...G}} D-glucose [[Image:LBGAxx1Glc.png|95px|link=https://lipidbank.jp/wiki/Volatile:ListMol?my_1=LBGA...G]]<br/>and D-galactose [[Image:LBGAxx1Gal.png|80px|link=https://lipidbank.jp/wiki/Volatile:ListMol?my_1=LBGA...G]] (&beta;)
|-
|-                 
|[[Volatile:ListMol?my_1=LBGA...M|M:]] including mannose<br/>[[Image:LBGAxx1M.png]]
|{{#volatile:ListMol|M:|LBGA...M}} including D-mannose<br/>[[Image:LBGAxx1M.png|80px|link=https://lipidbank.jp/wiki/Volatile:ListMol?my_1=LBGA...M]] (&alpha;)
|-
|-                 
|[[Volatile:ListMol?my_1=LBGA...L|L:]] including gulose<br/>[[Image:LBGAxx1L.png]]
|{{#volatile:ListMol|L:|LBGA...L}} including L-gulose<br/>[[Image:LBGAxx1L.png|90px|link=https://lipidbank.jp/wiki/Volatile:ListMol?my_1=LBGA...L]] (&beta;)
|-
|-                 
|[[Volatile:ListMol?my_1=LBGA...S|S:]] including HSO<sub>3</sub><br/>[[Image:LBGAxx1S.png]]
|{{#volatile:ListMol|S:|LBGA...S}} including HSO<sub>3</sub><br/>[[Image:LBGAxx1S.png|110px|link=https://lipidbank.jp/wiki/Volatile:ListMol?my_1=LBGA...S]]
|-
|-                 
|[[Volatile:ListMol?my_1=LBGA...X|X:]] others (glucosamine, methyl group etc.)
|{{#volatile:ListMol|X:|LBGA...X}} others (glucosamine etc.)
|}
|}
|}
|}
</center>
</center>


===References (文献一覧)===
=={{Bilingual|種・構造対応|Species-Structure Relationship}}==
; [[Volatile:ListRefOfID|LBGA|Reference|{{Bilingual|全ての文献をみる|Show all references}}]]
 
* [[Index:LBGA|{{Bilingual|登録されている属一覧|List of genera in this database}}]]


<center>
<center>
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|-
|-
{{#replace:
{{#replace:
{{#lua:
{{#invoke:LBGA|Species2Structure_Relationship|{{#var:allRefs}}}}
  function createBucket() return { {A={},C={} },{ N={},I={} },{ G={},X={} } } end
  desulfurococcales = createBucket()
  sulfolobales = createBucket()
  thermoproteales = createBucket()
  thermococcales = createBucket()
  thermoplasmatales = createBucket()
  halobacteriales = createBucket()
  methanobacteriales = createBucket()
  methanococcales = createBucket()
  methanomicrobiales = createBucket()
  methanopyrales = createBucket()
  methanosarcinales = createBucket()
 
  function printRow(name, T, reg)
    if (string.find(name, "halobacter") ~= nil)
      then print('\n&- align="right" style="background-color:#ddf"')
    elseif (string.find(name, "methano") == nil)
      then print('\n&- align="right" style="background-color:#fdd"')
    else
      print('\n&- align="right"')
    end
    if (string.find(name, "desulfurococcales") ~= nil)
      then print('& rowspan="3" style="background-color:#ddd" & <b>crenarchaeota</b>') end
    if (string.find(name, "thermococcales") ~= nil)
      then print('& rowspan="8" style="background-color:#ddd" & <b>euryarchaeota</b>') end
    print("&[[Volatile:ListMolByReference&"..reg.."&"..name.."]] && ")
    print(table.getn(T[1]["A"]).."\n&&"..table.getn(T[1]["C"]).."\n&&") T[1]["A"] = nil T[1]["C"] = nil
    for k,v in pairs(T[1]) do print(k.."("..table.getn(v)..") ") end print(" && ")
    print(table.getn(T[2]["N"]).."\n&&"..table.getn(T[2]["I"]).."\n&&") T[2]["N"] = nil T[2]["I"] = nil
    for k,v in pairs(T[2]) do print(k.."("..table.getn(v)..") ") end print(" && ")
    print(table.getn(T[3]["G"]).."\n&&"..table.getn(T[3]["X"]).."\n&&") T[3]["G"] = nil T[3]["X"] = nil
    for k,v in pairs(T[3]) do print(k.."("..table.getn(v)..") ") end
  end
  function addTable(T, id)
    exist = false
    for k,v in pairs(T) do if (id == v) then exist = true end end
    if (not exist) then table.insert(T, id) end
    end
 
  function register(T, id)
    local s = string.sub(id,5,5)
    if (T[1][s] == nil) then T[1][s] = {} end addTable(T[1][s], id)
    s = string.sub(id,6,6)
    if (T[2][s] == nil) then T[2][s] = {} end addTable(T[2][s], id)
    s = string.sub(id,8,8)
    if (T[3][s] == nil) then T[3][s] = {} end addTable(T[3][s], id)
  end
 
  for ref, sp, id in stdin:gmatch("&?&?([%w\. ]+)&&([%w]+)[%w\., ]+&&([^\n]+)") do
    if (string.match(sp,"Aeropyrum") or string.match(sp,"Desulfurococcus") or string.match(sp,"Pyrolobus"))
      then register(desulfurococcales, id)
    elseif (string.match(sp,"Acidianus") or string.match(sp,"Sulfolobus") or string.match(sp,"Desulfurolobus"))
      then register(sulfolobales, id)
    elseif (string.match(sp,"Pyrobaculum") or string.match(sp,"Thermoproteus"))
      then register(thermoproteales, id)
    elseif (string.match(sp,"Pyrococcus") or string.match(sp,"Thermococcus"))
      then register(thermococcales, id)
    elseif (string.match(sp,"Thermoplasma"))
      then register(thermoplasmatales, id)
    elseif (string.match(sp,"Haloarcula") or string.match(sp,"Halobacterium") or string.match(sp,"Halococcus") or string.match(sp,"Haloferax") or string.match(sp,"Halorubrum") or string.match(sp,"Natrialba") or string.match(sp,"Natronobacterium") or string.match(sp,"Natronococcus") or string.match(sp,"Halarchaeum"))
      then register(halobacteriales, id)
    elseif (string.match(sp,"Methanothermobacter") or string.match(sp,"Methanobrevibacter") or string.match(sp,"Methanosphaera") or string.match(sp,"Methanothermobacter"))
      then register(methanobacteriales, id)
    elseif (string.match(sp,"Methanothermococcus") or string.match(sp,"Methanococcus") or string.match(sp,"Methanocaldococcus"))
      then register(methanococcales, id)
    elseif (string.match(sp,"Methanomicrobium") or string.match(sp,"Methanospirillum"))
      then register(methanomicrobiales, id)
    elseif (string.match(sp,"Methanopyrus"))
      then register(methanopyrales, id)
    elseif (string.match(sp,"Methanococcoides") or string.match(sp,"Methanohalophilus") or string.match(sp,"Methanolobus") or string.match(sp,"Methanosarcina"))
      then register(methanosarcinales, id)
    end
  end
  printRow("desulfurococcales", desulfurococcales, "Aeropyrum~Desulfurococcus~Pyrolobus")
  printRow("sulfolobales",sulfolobales, "Acidianus~Sulfolobus~Desulfurolobus")
  printRow("thermoproteales",thermoproteales, "Pyrobaculum~Thermoproteus")
  printRow("thermococcales",thermococcales, "Pyrococcus~Thermococcus")
  printRow("thermoplasmatales",thermoplasmatales, "Thermoplasma")
  printRow("halobacteriales",halobacteriales, "Haloarcula~Halobacterium~Halococcus~Haloferax~Halorubrum~Natrialba~Natronobacterium~Natronococcus~Halarchaeum")
  printRow("methanobacteriales",methanobacteriales, "Methanothermobacter~Methanobrevibacter~Methanosphaera")
  printRow("methanococcales",methanococcales, "Methanothermococcus~Methanococcus~Methanocaldococcus")
  printRow("methanomicrobiales",methanomicrobiales, "Methanomicrobium~Methanospirillum")
  printRow("methanopyrales",methanopyrales, "Methanopyrus")
  printRow("methanosarcinales",methanosarcinales, "Methanococcoides~Methanohalophilus~Methanolobus~Methanosarcina")
|
{{#var:allRefs}}
}}
|&|{{#bar:}}}}
|&|{{#bar:}}}}
|}
|}
Line 322: Line 235:


;{{Bilingual|登録された菌種|Registered Species}}
;{{Bilingual|登録された菌種|Registered Species}}
{{#lua:
{{#invoke:LBGA|RegisteredSpecies|{{#var:allRefs}}}}
  isIn = {} T = {}
 
  for ref, sp, id in stdin:gmatch("&?&?([%w\. ]+)&&([%w]+)[%w\., ]*&&([^\n]+)") do
 
    if (isIn[sp] == nil) then isIn[sp] = true table.insert(T, sp) end
==References==
  end
 
  table.sort(T)
* {{#volatile:ListRefOfID|{{Bilingual|全ての文献をみる|Show all references}}|LBGA|Reference}}
  s = ""
  for i,v in pairs(T) do
    s = s .. "[[Volatile:ListMolByReference?my_1=" .. v .. "{{#bar:}}" .. v .. "]] "
  end
  print(s)
|
{{#var:allRefs}}
}}


==生合成==
==生合成==
Line 344: Line 249:




;参考情報
<references/>
 
=={{Bilingual|環境マーカー|Environmental Markers}}==
 
;{{Bilingual|海底|Marine Sediments}}
{{Twocolumn
|From marine sediment samples, <sup>13</sup>C-depleted archaeol and &beta;-hydroxy archaeol are found with 16S rRNA of Methanomicrobiales and Methanosarcinales <ref>Hinrichs KU et al. (1999) Nature 398, 802 PMID 10235261</ref>. Such archea is considered to oxidize methane anaerobically, forming consortia with sulfate-reducing bacteria <ref>Orphan VJ et al. (2001) Appl. Environ. Microbiol. 67, 1922 PMID 11282650</ref>.
|海底では Methanomicrobiales, Methanosarcinales の 16S rRNA とともに <sup>13</sup>C が含まれないアーキオール、&beta;ヒドロキシアーキオールが見出されます。硫酸還元菌と共生する形でメタンを資化するアーキアが多く存在すると考えられています。
}}
 
 
<references/>
<references/>


Latest revision as of 02:11, 31 January 2023

Archaeal Lipid


Upper classes: LB LBG

Class Overview

Archaeal lipid is composed of sn-glycerol 1-phosphate and ether-linked isoprenoids (C20 phytanes). This composition is different from lipids in eubacteria and eukaryotes, which comprise of sn-glycerol 3-phosphate and ester-linked fatty acids. Responsible biosynthetic enzymes are also non-homologous. Archaea also contains tetraether lipids in which two isoprenes (C40 biphytanes) are ether-linked with two glycerols at both ends (caldarchaeol).

アーキア[1]の脂質は、 sn-グリセロール1リン酸にメバロン酸由来のイソプレン骨格（C20フィタン）がエーテル結合しています (snがわからない人は異性体のページを参照してください)。 これは、グリセロール3リン酸と脂肪酸を利用する真正細菌や真核生物と全く異なる構造で、生合成をおこなう酵素も相同ではありません。またテトラエーテル型と呼ばれる、長さ40のバイフィタンが末端で2分子のグリセロールとエーテル結合した環状脂質（カルドアーキオール）も広く存在します。

  1. ↑ 古細菌と呼ばれることが多いのですが、真正細菌と明確に区別するためにここではアーキアと記します。

Phylogeny

Archaea are separated into two major phyla (Crenarchaeota and Euryarchaeota)[1] and three ecologically different microbes exist: thermophile, halophile, and methanogen (Table 1). Previously archaea were believed to exist only in extreme environments, but their habitat is actually ubiquitous from sea surface to deep underground. Genus names are summarized here.

アーキアは大きくCrenarchaeotaとEuryarchaetaという二大グループに分かれ[2]、 アンモニア酸化菌、好熱菌、好塩菌、メタン生成菌の４種類が含まれます（表1）。以前は極限環境に住むと考えられていましたが、特にアンモニア酸化菌 (thaumarchaeota) は海から地底まで遍在することがわかっています。属名一覧は別ページにまとめています。

Table 1. Clades in Archaea
Phyrum (綱) Order (目) Family (科) Character Gram-staining
thaumarchaeota cenarchaeales cenarchaeaceae ammonia oxidizer ? (unculturable)
crenarchaeota desulfurococcales desulfurococcaceae, pyrodictiaceae Non-methanogenic
(hyper) thermophils 		negative
sulfolobales sulfolobaceae
thermoproteales thermoproteaceae
euryarchaeota thermococcales thermococcaceae
thermoplasmatales thermoplasmataceae
halobacteriales halobacteriaceae Halophils negative
methanobacteriales methanobacteriaceae, methanothermaceae Methanogens mostly positive
methanococcales methanococcaceae, methanocaldococcaceae
methanomicrobiales methanomicrobiaceae, methanospirillaceae
methanopyrales methanopyraceae
methanosarcinales methanosarcinaceae, methanosaetaceae
  1. ↑ Studies on mostly uncultured archaea identified other small phyla such as Korarchaeota (Barns et al. 1996 PMID 8799176), Nanoarchaeota (Huber et al. 2002 PMID 11986665), and the Thaumarchaeota (Brochier-Armanet et al. 2002 PMID 18274537). They are characterized only by genome sequences and not considered here.
  2. ↑ 難培養性のアーキアとしてKorarchaeota (Barns et al. 1996 PMID 8799176), Nanoarchaeota (Huber et al. 2002 PMID 11986665), Thaumarchaeota (Brochier-Armanet et al. 2002 PMID 18274537)などの小グループも見つかっていますが難培養性でゲノム解析のみのため、生物分類上は確定していません。

Nomenclature

Much of archaeal lipid were named by a Japanese research group[1]. Note that sn-1 position of glycerol is at the bottom of the pictures and the ether bond at the sn-2 position is below the paper plane.

アーキア脂質の名称の多くは日本人によって名付けられました。以下の図ではグリセロールの sn-1 位が 下側で-OH として表示されています。sn-2 位の水酸基は紙面の奥側です。通常のグリセロ脂質の描き方とは向きが異なるので注意してください。

Archaeol (= 2,3-di-O-alkyl sn-glycerol diether) LBGAA.png
C20/20, C25/20, C25/25

The alkyl chain is C20-isoprane (Sehgal et al 1962 [2]). Archaetidic acid refers to its monophophate ether.

アルキル基はC20のイソプラン（飽和イソプレン）。Archaetidic acid はその1リン酸エステルです。

Caldarchaeol LBGAC.png

An tetraether where 2 glycerol molecules are connected with 2 alkanediols at sn-2 and sn-3 positions. Langworthy found the structure from Thermoplasma acidophilum in 1977. Its name "cald" (i.e. hot) originates its discovery from a hyperthermophil.

2分子のグリセロールがsn-2, sn-3 位でアルカンジオールとエーテル結合したテトラエーテル。Langworthy が Thermoplasma acidophilum より発見し、超高熱菌から見出されたため cald (ラテン語で「熱い」) の名前がつきます。

Calditocaldarchaeol LBGAD.png

Calditol refers to a 5-carbon cyclic polyol [ 2-hydroxymethyl 1-(dihydroxypropoxy) 2,3,4,5-cyclopentanetetraol ] , which is connected to sn-1 glycerol by an ether linkage. It was first identified from Caldariella acidophila (now Sulfolobus solfataricus) and was called nonitol with a wrong structure. Bleriot et al., 2002).[3] shows its brief history.

カルジトールは水酸基を5つ有する炭素五員環で、sn-1部位でグリセロールにエーテル結合しています。当初 Caldariella acidophila MT-4 (現 Sulfolobus solfataricus) に見出された際に異なる構造が報告され nonitol と呼ばれた時期もありました。下のBleriotらの論文に経緯があります。

(Macro)Cyclic Archaeol LBGAY.png

(Macro)Cyclic archaeol is characteristic to thermophilic archaea such as M. jannaschii. It is believed to increase membrane rigidity under higher pressure. Its amount is reported to increase in cultures of high temperature or pressure. [4][5]

環状アーキオールは好熱菌 M. jannaschii にみられ、膜構造の強度を増すと考えられています。生育温度の上昇、または圧力の上昇で量が増えると報告されています。

  1. ↑ Nishihara M, Morii H, Koga Y (1987) Structure determination of a quartet of novel tetraether lipids from Methanobacterium thermoautotrophicum. J Biochem 101:1007-1015 PMID 3611039
  2. ↑ Few species contain C25/25 or C20/25 isopranoids.
  3. ↑ Bleriot Y, Untersteller E, Fritz B, Sinay P (2002) Total Synthesis of calditol: Structural clarification of this typical component of archaea order Sulfolobales. Chemistry 8(1):240-246 PMID 11822455
  4. ↑ Sprott GD, Meloche M, Richards JC (1991) Proportions of diether, macrocyclic diether, and tetraether lipids in Methanococcus jannaschii grown at different temperatures. J Bacteriol 173, 3907-3910 PMID 2050642
  5. ↑ Kaneshiro SM, Clark DS (1995) Pressure effects on the composition and thermal behavior of lipids from the deep-sea thermophile methanococcus jannaschii. J Bacteriol 177, 3668-3672 PMID 7601829

Design of Page Titles

Archaeal lipid is categorized in glycerolipid (LBG). Each ID contains information on the core-lipid type, chemical modification of polar head, and attached sugars.

古細菌の脂質はグリセロ脂質 (LBG) に含まれます。各分子のページIDは基本骨格、極性基のタイプ、糖のタイプがコード化されています。

10-DIGIT

L B G A x y z w c c

  • x ... core-lipid structure (one of A H U C D Y)
  • y ... polar-head category (one of N P C E I S G A X)
  • z ... total number of sugars (Inositol and standard hexose are counted. Calditol is not counted.)
  • w ... sugar type (one of N G M L S X)
  • c ... serial number

  • x ... コアリピッド構造
  • y ... 極性基（リン酸部分）の構造
  • z ... 糖の個数
  • w ... 糖のタイプ
  • c ... 通し番号

Classification 分類

Core Lipid Structure 基本構造

Core-lipid Structure
A: archaeol
LBGAA.png

LBGAH.png

LBGAU.png
C: caldarchaeol (tetraether type)
LBGAC.png
D: irregular caldarchaeol (e.g. calditocald- or crenarchaeol, trialkyl or H-shaped archaeol)
LBGAD.png

LBGAY.png
Polar-head Type
no group
saccharides
phosphate or alcohol
LBGAxP.png
phosphocholine
LBGAxC.png
phosphoethanolamine
LBGAxE.png
phosphoinositol
LBGAxI.png
phosphoserine
LBGAxS.png
phosphoglycerol
LBGAxG.png
aminopentanetetrol
LBGAxA.png
others
Sugar Type
inositol only or no sugar
D-glucose LBGAxx1Glc.png
and D-galactose LBGAxx1Gal.png (β)
including D-mannose
LBGAxx1M.png (α)
including L-gulose
LBGAxx1L.png (β)
including HSO3
LBGAxx1S.png
others (glucosamine etc.)

Species-Structure Relationship


Registered Number of Lipid Molecules (Total: 162)
Phylum Order Core-lipid Polar-head Sugar
ArOH CArOH others None Ino others Glc,Gal Gro etc others
thaumarchaeota
0 0 D(1) 0 0 B(1) 0 0 N(1)
crenarchaeota
2 4 1 4 B(1) 3 0 N(3)
4 11 D(7) 7 9 B(4) E(1) G(1) 8 0 S(4) N(10)
0 11 8 3 11 0
euryarchaeota
6 1 D(2) 1 1 P(1) B(4) X(1) G(1) 1 0 N(8)
2 20 D(2) 12 0 B(4) G(8) 3 0 M(1) L(13) N(7)
28 0 U(5) 15 0 X(1) B(5) P(2) G(10) 1 0 S(9) M(5) N(18)
14 15 H(3) U(3) 4 5 A(2) P(5) S(4) B(4) E(6) G(3) X(2) 10 0 N(25)
4 1 H(2) Y(5) 5 0 X(1) B(5) E(1) 5 1 N(6)
6 12 7 0 B(3) A(4) G(4) 13 0 N(5)
3 0 U(4) 0 1 C(4) B(1) E(1) 0 0 N(7)
6 1 H(7) U(3) 0 4 P(1) S(1) B(6) E(2) G(3) 0 1 N(16)
Registered Species


References

生合成

  1. グリセロールははじめ sn-グリセロール 3リン酸 (G3P) から出発し、2位の脱水素（ケトン化）を経て sn-グリセロール 1リン酸 (G1P) になります。[1]
  2. メバロン酸由来で合成されたゲラニルゲラニルピロリン酸（またはフィチルピロリン酸）の1位の炭素がグリセロールの酸素に求核攻撃してエーテル結合を作ります。[2]
  3. 不飽和のアルキル基を飽和化し、各種の極性基や糖鎖が結合します。


  1. ↑ 中間体はジヒドロキシアセトンリン酸と考えられます。反転の時点でG3Pの1位がモノアルキル化されている可能性もあります。
  2. ↑ グリセロールの1,3位に18Oを入れるとアーキオールでも保存されることが示されています。

Environmental Markers

Marine Sediments

From marine sediment samples, 13C-depleted archaeol and β-hydroxy archaeol are found with 16S rRNA of Methanomicrobiales and Methanosarcinales [1]. Such archea is considered to oxidize methane anaerobically, forming consortia with sulfate-reducing bacteria [2].

海底では Methanomicrobiales, Methanosarcinales の 16S rRNA とともに 13C が含まれないアーキオール、βヒドロキシアーキオールが見出されます。硫酸還元菌と共生する形でメタンを資化するアーキアが多く存在すると考えられています。


  1. ↑ Hinrichs KU et al. (1999) Nature 398, 802 PMID 10235261
  2. ↑ Orphan VJ et al. (2001) Appl. Environ. Microbiol. 67, 1922 PMID 11282650

分析法

Bligh and Dyer extraction (all lipids)
Arrow00d35.png 55% HI
Arrow00d35.png acetic
anhydride
Arrow00d.png 46% HF
0.18% HCl-
methanol
9-AN-
DMAP-CCl4
Arrow00d35.png 5% HCl-
methanol
Arrow00d.png BCl3
alkyl iodide acetylated core lipid methylated sugars & Pho-inositol
Arrow00d35.png LiAH4
Arrow00d35.png 5% HCl-
methanol
Arrow00d35.png 1M HCl Arrow00d35.png 6M HCl
carbohydrate core lipids core lipids (OH-ArOH etc.) sugars inositol Pho-glycerols
GC 分析 TLC 分析 HPLC 分析 GC 分析 GC 分析 電気泳動、TLC 分析

Subcategories

This category has the following 4 subcategories, out of 4 total.

L

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