Category:LBA: Difference between revisions
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==={{Bilingual|脂質命名法|Nomenclature}}===
==={{Bilingual|脂質命名法|Nomenclature}}===
{{Bilingual|
{{Twocolumn|
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", Journal of Biochemistry 101:1007-1015</ref>.
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", Journal of Biochemistry 101:1007-1015</ref>.
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|-
!Archaeol (= 2,3-di-O-alkyl sn-glycerol diether) [[Image:LBAA.png]]
!Archaeol (= 2,3-di-O-alkyl sn-glycerol diether) [[Image:LBAA.png]]
|
|{{Twocolumn
{{Bilingual|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。
|The alkyl chain is either C20- or C25-isoprene. 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。
The alkyl chain is either C20- or C25-isoprene. Archaetidic acid refers to its monophophate ether.
}}
}}
|-
|-
!Caldarchaeol [[Image:LBAC.png]]
!Caldarchaeol [[Image:LBAC.png]]
|
|{{Twocolumn
{{Bilingual|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 (= hot) の名前がつく
|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.
|
|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。
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" (=hot) in its name.
}}
}}
|-
|-
!Isocaldarchaeol [[Image:LBAI.png]]
!Isocaldarchaeol [[Image:LBAI.png]]
|
|{{Twocolumn
{{Bilingual|片方のグリセロールがCaldarchaeolと向きの違う異性体
|A geometric isomer of caldarchaeol where the alkanediols connect sn-2 and sn-2 (or sn-3 and sn-3) positions.
|
|片方のグリセロールがCaldarchaeolと向きの違う異性体
A geometric isomer of caldarchaeol where the alkanediols connect sn-2 and sn-2 (or sn-3 and sn-3) positions.
}}
}}
|-
|-
! Calditocaldarchaeol [[Image:LBAD.png]]
! Calditocaldarchaeol [[Image:LBAD.png]]
|
|{{Twocolumn
{{Bilingual|カルジトールは水酸基を5つ有する炭素五員環がsn-1部位でグリセロールにエーテル結合した構造。以前は異なる構造が報告されており nonitol と呼ばれた時期もあった
|Calditol refers to a 5-carbon cyclic polyol 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</ref>)
|
|カルジトールは水酸基を5つ有する炭素五員環がsn-1部位でグリセロールにエーテル結合した構造。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。
Calditol refers to a 5-carbon cyclic polyol connected to sn-1 glycerol by an ether linkage. It was once called nonitol and the structure was also considered different.<ref>Bleriot Y, Untersteller E, Fritz B, Sinay P "Total Synthesis of calditol: Structural clarification of this typical component of archaea order Sulfolobales", Chemistry, 8(1):240-246</ref>
}}
}}
|}
|}

Revision as of 06:18, 11 March 2013

Archaeal Lipid


Upper classes: LB

Class Overview

Archaeal lipid is composed of sn-glycerol 1-phosphate and isoprenoids. This composition is different from lipid in eubacteria and eukaryotes, which comprises of sn-glycerol 3-phosphate and fatty acids. Responsible enzymes are also non-homologous. Archaea also contains tetraether lipid

アーキア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。の脂質は、 sn-グリセロール1リン酸にイソプレン骨格がエーテル結合しています。 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重合した環状脂質も広く存在し、これが単分子膜を形成すると考えられています。


Phylogeny

Archaea are separated into two phyla which show three different characters (Table 1: leftmost column).

アーキアはcrenarchaeotaとeuryarchaetaに分かれますが、 特徴からみると三通りになります（表の最左カラム）。

Table 1. Clades in Archaea
Character Phyrum (綱) Order (目) Family (科)
Non-methanogenic
hyperthermophils 		crenarchaeota desulfurococcales desulfurococcaceae, pyrodictiaceae
sulfolobales sulfolobaceae
thermoproteales thermoproteaceae
euryarchaeota thermococcales thermococcaceae
thermoplasmatales thermoplasmataceae
Halophils halobacteriales halobacteriaceae
Methanogens methanobacteriales methanobacteriaceae, methanothermaceae
methanococcales methanococcaceae, methanocaldococcaceae
methanomicrobiales methanomicrobiaceae, methanospirillaceae
methanopyrales methanopyraceae
methanosarcinales methanosarcinaceae, methanosaetaceae

Nomenclature

Much of archaeal lipid were named by a Japanese research group[1].

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。

Archaeol (= 2,3-di-O-alkyl sn-glycerol diether) File:LBAA.png

The alkyl chain is either C20- or C25-isoprene. 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。

Caldarchaeol File:LBAC.png

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.

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。

Isocaldarchaeol File:LBAI.png

A geometric isomer of caldarchaeol where the alkanediols connect sn-2 and sn-2 (or sn-3 and sn-3) positions.

片方のグリセロールがCaldarchaeolと向きの違う異性体

Calditocaldarchaeol File:LBAD.png

Calditol refers to a 5-carbon cyclic polyol 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).[2])

カルジトールは水酸基を5つ有する炭素五員環がsn-1部位でグリセロールにエーテル結合した構造。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。

  1. ↑ Nishihara M, Morii H, Koga Y (1987) "Structure determination of a quartet of novel tetraether lipids from Methanobacterium thermoautotrophicum", Journal of Biochemistry 101:1007-1015
  2. ↑ 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

Design of Fat acyl Page Titles

Each ID contains information on backbone type, chemical modification of polar head, and attached sugars.

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。

9-DIGIT

L B A x y z w c c

  • x ... backbone type
  • y ... polar-head type
  • z ... sugar type
  • w ... number of sugars
  • c ... serial number

  • x ... バックボーンの構造
  • y ... 極性基（リン酸部分）の構造
  • z ... 糖のタイプ
  • w ... 糖の個数
  • c ... 通し番号

Classification 分類

Backbone Structure 基本構造

Backbone Structure
A: archaeol (C20,C20 type below)
File:LBAA.png
H: hydroxy & methoxy archaeol (sn-2-hydroxy below)
File:LBAH.png
U: unsaturated (alkenyl) archaeol
File:LBAU.png
C: caldachaeol (tetraether type)
File:LBAC.png
D: calditocaldarchaeol
File:LBAD.png
Y: cyclic archaeol
File:LBAY.png
Order Backbone (see left) Polar-head Sugar

{{#lua: 

 desulfurococcales ={{},{},{}}
 sulfolobales ={{},{},{}}
 thermoproteales ={{},{},{}}
 thermococcales ={{},{},{}}
 thermoplasmatales ={{},{},{}}
 halobacteriales ={{},{},{}}
 methanobacteriales ={{},{},{}}
 methanococcales ={{},{},{}}
 methanomicrobiales ={{},{},{}}
 methanopyrales ={{},{},{}}
 methanosarcinales ={{},{},{}}

 function printRow(name, T, reg) print("\n|-\n|"..reg.."|"..name.." || ") for k,v in pairs(T[1]) do print(k.."("..v..") ") end print(" || ") for k,v in pairs(T[2]) do print(k.."("..v..") ") end print(" || ") for k,v in pairs(T[3]) do print(k.."("..v..") ") end end
 
 function register(T, id) local s = string.sub(id,4,4) if (T[1][s] == nil) then T[1][s]=1 else T[1][s]= T[1][s] + 1 end s = string.sub(id,5,5) if (T[2][s] == nil) then T[2][s]=1 else T[2][s]= T[2][s] + 1 end s = string.sub(id,6,6) if (T[3][s] == nil) then T[3][s]=1 else T[3][s]= T[3][s] + 1 end end

 for ref, sp, id in stdin:gmatch("|?|?([%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"))
     then register(halobacteriales, id)
   elseif (string.match(sp,"Methanobacterium") 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")
 printRow("methanobacteriales",methanobacteriales, "Methanobacterium~Methanobrevibacter~Methanosphaera~Methanothermobacter")
 printRow("methanococcales",methanococcales, "Methanothermococcus~Methanococcus~Methanocaldococcus")
 printRow("methanomicrobiales",methanomicrobiales, "Methanomicrobium~Methanospirillum")
 printRow("methanopyrales",methanopyrales, "Methanopyrus")
 printRow("mehtanosarcinales",methanosarcinales, "Methanococcoides~Methanohalophilus~Methanolobus~Methanosarcina")

}}

Polar-head Type
N: no structure; P: phosphate; C: phosphocholine; E: phosphoethanolamine; I: phosphoinositol; S: phosphoserine; G: phosphoglycerol; A: aminopentanetetrol; X: others
Sugar Type
G: glucose and galactose; M: including mannose; L: including gulose; S: including HSO3; X: others;

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