Category:LBA: Difference between revisions

Revision as of 07:02, 14 March 2013

Archaeal Lipid

Upper classes: LB

Class Overview

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).

アーキア^[1]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。

↑ 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。

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)

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

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

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

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。

↑ 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
↑ 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

Archaeal lipid is categorized in glycerolipid (LBG). Each ID contains information on backbone 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。

9-DIGIT

L

B

G

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

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;

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")

}}

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[1] 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。

[2] 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

[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

[1]

[1]

[2]

@@ Line 64: / Line 64: @@
 {|
 |-
-!Archaeol (= 2,3-di-O-alkyl sn-glycerol diether) [[Image:LBAA.png]]
+!Archaeol (= 2,3-di-O-alkyl sn-glycerol diether) [[Image:LBGAA.png]]
 |{{Twocolumn
 |The alkyl chain is either C20- or C25-isoprene. Archaetidic acid refers to its monophophate ether.
@@ Line 70: / Line 70: @@
 }}
 |-
-!Caldarchaeol [[Image:LBAC.png]]
+!Caldarchaeol [[Image:LBGAC.png]]
 |{{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.
@@ Line 76: / Line 76: @@
 }}
 |-
-!Isocaldarchaeol [[Image:LBAI.png]]
+!Isocaldarchaeol [[Image:LBGAI.png]]
 |{{Twocolumn
 |A geometric isomer of caldarchaeol where the alkanediols connect sn-2 and sn-2 (or sn-3 and sn-3) positions.
@@ Line 82: / Line 82: @@
 }}
 |-
-! Calditocaldarchaeol [[Image:LBAD.png]]
+! Calditocaldarchaeol [[Image:LBGAD.png]]
 |{{Twocolumn
 |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>)
@@ Line 93: / Line 93: @@
 =={{Bilingual|ID番号 (ページ名) の設計|Design of Fat acyl Page Titles}}==
 {{Twocolumn|
-Each ID contains information on backbone type, chemical modification of polar head, and attached sugars.
+Archaeal lipid is categorized in glycerolipid (LBG). 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。
+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。
 }}
 <center>
@@ Line 103: / Line 103: @@
 <td style="background-color:yellowgreen;" width=15px align="center"><big>L</big>
 <td style="background-color:yellowgreen;" width=15px align="center"><big>B</big>
+<td style="background-color:yellowgreen;" width=15px align="center"><big>G</big>
 <td style="background-color:darkseagreen;" width=15px align="center"><big>A</big>
 <td style="background-color:tomato; color:white" width=15px align="center"><big>''x''</big>
@@ Line 137: / Line 138: @@
 ! Backbone Structure
 |- valign="top"
-|[[Volatile:ListMol?my_1=LBAA|A: archaeol]] (C20,C20 type below) <br/>[[Image:LBAA.png]]
+|[[Volatile:ListMol?my_1=LBGAA|A: archaeol]] (C20,C20 type below) <br/>[[Image:LBAA.png]]
 |-
-|[[Volatile:ListMol?my_1=LBAH|H: hydroxy & methoxy archaeol]] (sn-2-hydroxy below) <br/>[[Image:LBAH.png]]
+|[[Volatile:ListMol?my_1=LBGAH|H: hydroxy & methoxy archaeol]] (sn-2-hydroxy below) <br/>[[Image:LBAH.png]]
 |-
-|[[Volatile:ListMol?my_1=LBAU|U: unsaturated (alkenyl) archaeol]]<br/>[[Image:LBAU.png]]
+|[[Volatile:ListMol?my_1=LBGAU|U: unsaturated (alkenyl) archaeol]]<br/>[[Image:LBAU.png]]
 |-
-|[[Volatile:ListMol?my_1=LBAC|C: caldachaeol]] (tetraether type)<br/>[[Image:LBAC.png]]
+|[[Volatile:ListMol?my_1=LBGAC|C: caldachaeol]] (tetraether type)<br/>[[Image:LBAC.png]]
 |-
-|[[Volatile:ListMol?my_1=LBAD|D: calditocaldarchaeol]]<br/>[[Image:LBAD.png]]
+|[[Volatile:ListMol?my_1=LBGAD|D: calditocaldarchaeol]]<br/>[[Image:LBAD.png]]
 |-
-|[[Volatile:ListMol?my_1=LBAY|Y: cyclic archaeol]]<br/>[[Image:LBAY.png]]
+|[[Volatile:ListMol?my_1=LBGAY|Y: cyclic archaeol]]<br/>[[Image:LBAY.png]]
 |}