Category:LBA: Difference between revisions

Revision as of 05:53, 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

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.
Caldarchaeol File:LBAC.png	An tetraether where 2 glycerol molecules are connected with 2 alkanediols at sn-2 and sn-3 positions.
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.
Calditocaldarchaeol File:LBAD.png	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.

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

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;

This category currently contains no pages or media.

@@ Line 57: / Line 57: @@
 ==={{Bilingual|脂質命名法|Nomenclature}}===
+{{Bilingual|
+Much of archaeal lipid were named by a Japanese research group.
+|
 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 [[Image:LBAA.png]]
+!Archaeol (= 2,3-di-O-alkyl sn-glycerol diether) [[Image:LBAA.png]]
-| 2,3-di-O-alkyl sn-glycerol diether のこと。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。
+|
+{{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.
+}}
 |-
-| Caldarchaeol [[Image:LBAC.png]]
+!Caldarchaeol [[Image:LBAC.png]]
-| 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。
+|
+{{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
+|
+An tetraether where 2 glycerol molecules are connected with 2 alkanediols at sn-2 and sn-3 positions.
+}}
 |-
-| Isocaldarchaeol [[Image:LBAI.png]]
+!Isocaldarchaeol [[Image:LBAI.png]]
-| 片方のグリセロールがCaldarchaeolと向きの違う異性体
+|
+{{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.
+}}
+|-
+! Calditocaldarchaeol [[Image:LBAD.png]]
+|
+{{Bilingual|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をカルジトールと呼びます。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りました
+|
+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.
+}}
 |}