Category:LBA: Difference between revisions
Line 164: Line 164:
!colspan="3"| Sugar
!colspan="3"| Sugar
|-
|-
! A || C || others || N || I || others || G || X || others
! ArOH || CArOH || others || None || Ino || others || Glc,Gal || Gro etc || others
|-
|-
{{#replace:
{{#replace:
{{#lua:
{{#lua:
   desulfurococcales ={{A=0,C=0},{N=0,I=0},{G=0,X=0}}
   function createBucket() return {{A=0,C=0},{N=0,I=0},{G=0,X=0}} end
   sulfolobales ={{A=0,C=0},{N=0,I=0},{G=0,X=0}}
  desulfurococcales = createBucket()
   thermoproteales ={{A=0,C=0},{N=0,I=0},{G=0,X=0}}
   sulfolobales = createBucket()
   thermococcales ={{A=0,C=0},{N=0,I=0},{G=0,X=0}}
   thermoproteales = createBucket()
   thermoplasmatales ={{A=0,C=0},{N=0,I=0},{G=0,X=0}}
   thermococcales = createBucket()
   halobacteriales ={{A=0,C=0},{N=0,I=0},{G=0,X=0}}
   thermoplasmatales = createBucket()
   methanobacteriales ={{A=0,C=0},{N=0,I=0},{G=0,X=0}}
   halobacteriales = createBucket()
   methanococcales ={{A=0,C=0},{N=0,I=0},{G=0,X=0}}
   methanobacteriales = createBucket()
   methanomicrobiales ={{A=0,C=0},{N=0,I=0},{G=0,X=0}}
   methanococcales = createBucket()
   methanopyrales ={{A=0,C=0},{N=0,I=0},{G=0,X=0}}
   methanomicrobiales = createBucket()
   methanosarcinales ={{A=0,C=0},{N=0,I=0},{G=0,X=0}}
   methanopyrales = createBucket()
   methanosarcinales = createBucket()


   function printRow(name, T, reg) print("\n&- align='right'\n&[[Volatile:ListMolByReference&"..reg.."&"..name.."]] && ")
   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
    print("&[[Volatile:ListMolByReference&"..reg.."&"..name.."]] && ")
     print(T[1]["A"].."\n&&"..T[1]["C"].."\n&&") T[1]["A"] = nil T[1]["C"] = nil
     print(T[1]["A"].."\n&&"..T[1]["C"].."\n&&") T[1]["A"] = nil T[1]["C"] = nil
     for k,v in pairs(T[1]) do print(k.."("..v..") ") end print(" && ")
     for k,v in pairs(T[1]) do print(k.."("..v..") ") end print(" && ")
Line 189: Line 198:
   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
   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
   for ref, sp, id in stdin:gmatch("&?&?([%w\. ]+)&&([%w\., ]+)&&([^\n]+)") do
Line 226: Line 242:
   printRow("methanomicrobiales",methanomicrobiales, "Methanomicrobium~Methanospirillum")
   printRow("methanomicrobiales",methanomicrobiales, "Methanomicrobium~Methanospirillum")
   printRow("methanopyrales",methanopyrales, "Methanopyrus")
   printRow("methanopyrales",methanopyrales, "Methanopyrus")
   printRow("mehtanosarcinales",methanosarcinales, "Methanococcoides~Methanohalophilus~Methanolobus~Methanosarcina")
   printRow("methanosarcinales",methanosarcinales, "Methanococcoides~Methanohalophilus~Methanolobus~Methanosarcina")
|
|
{{#SearchLine:&&LBA|Reference}}
{{#SearchLine:&&LBA|Reference}}

Revision as of 22:21, 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。

  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。

Phylogeny

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

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1）。

Table 1. Clades in Archaea
Phyrum (綱) Order (目) Family (科) Character
crenarchaeota desulfurococcales desulfurococcaceae, pyrodictiaceae Non-methanogenic
(hyper) thermophils
sulfolobales sulfolobaceae
thermoproteales thermoproteaceae
euryarchaeota thermococcales thermococcaceae
thermoplasmatales thermoplasmataceae
halobacteriales halobacteriaceae Halophils
methanobacteriales methanobacteriaceae, methanothermaceae Methanogens
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) LBGAA.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 LBGAC.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 LBGAI.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 LBGAD.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

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。

10-DIGIT

L B G A x y z w c c

  • x ... backbone type
  • y ... polar-head type
  • z ... number of sugars
  • w ... sugar type
  • 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 ... 糖の個数
  • w ... 糖のタイプ
  • c ... 通し番号

Classification 分類

Backbone Structure 基本構造

Backbone Structure
A: archaeol (C20,C20 type below)
LBGAA.png
H: hydroxy & methoxy archaeol (sn-2-hydroxy below)
LBGAH.png
U: unsaturated (alkenyl) archaeol
LBGAU.png
C: caldachaeol (tetraether type)
LBGAC.png
D: calditocaldarchaeol
LBGAD.png
Y: cyclic archaeol
LBGAY.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;
{{#lua: function createBucket() return {{A=0,C=0},{N=0,I=0},{G=0,X=0}} 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 print("|"..reg.."|"..name.." || ") print(T[1]["A"].."\n||"..T[1]["C"].."\n||") T[1]["A"] = nil T[1]["C"] = nil for k,v in pairs(T[1]) do print(k.."("..v..") ") end print(" || ") print(T[2]["N"].."\n||"..T[2]["I"].."\n||") T[2]["N"] = nil T[2]["I"] = nil for k,v in pairs(T[2]) do print(k.."("..v..") ") end print(" || ") print(T[3]["G"].."\n||"..T[3]["X"].."\n||") T[3]["G"] = nil T[3]["X"] = nil 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("methanosarcinales",methanosarcinales, "Methanococcoides~Methanohalophilus~Methanolobus~Methanosarcina")
Order Backbone Polar-head Sugar
ArOH CArOH others None Ino others Glc,Gal Gro etc others

}}


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