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Categories of SUIT protocols

Description

Categories of SUIT protocols group SUIT protocols according to all substrate types involved in a protocol (F, N, S, Gp), independent of the sequence of titrations of substrates and inhibitors which define the Electron-transfer-pathway states. The N-type substrates are listed in parentheses, independent of the sequence of titrations. ROX states may or may not be included in a SUIT protocol, which does not change its category. Similarly, the CIV assay may or may not be added at the end of a SUIT protocol, without effect on the category of a SUIT protocol.

F - ET-pathway-level 5: FADH₂-linked substrates (FAO) with obligatory support by the N-linked pathway.
N - ET-pathway-level 4: NADH-linked substrates (CI-linked).
S - ET-pathway-level 3: Succinate (CII-linked).
Gp - ET-pathway-level 3: Glycerophosphate (CGpDH-linked).
Y(X)- In the SUIT general protocols Y makes reference to the ET-pathway state and X to the combination os substrates added for the corresponding pathway.

» MiPNet article

Abbreviation: SUIT-catg

Reference: MiPNet21.06 SUIT RP

MitoPedia concepts: SUIT concept

Categories of SUIT protocols and ET-pathway control states

Gnaiger E (2017) Categories of SUIT protocols and ETS pathway control states. MiPNet 2017-03-12; original 2016-03-20; edited 2016-08-21.

» MiPNet21.06 SUIT RP

Oroboros (2017) MiPNet

Abstract: The complexity of SUIT protocols is primarily determined by the large number of Electron transfer-pathway states and fuel substrates involved, compared to only three well defined coupling-control states. Whereas the SUIT protocol names specify all sequential steps in a SUIT protocol, the categories of SUIT protocols reduce this diversity to a list of substrate types involved.

• O2k-Network Lab: AT Innsbruck Oroboros

Labels: MiParea: Instruments;methods

Pathway: F, N, S, Gp, CIV, NS, Other combinations, ROX HRR: Theory

Towards a library of SUIT protocols

At the present stage of development of the Library of SUIT protocols as part of the MitoFit Quality Control System, the substrate types linked to five ET-pathway types are considered.

F-junction on the pathway level of converging FADH₂- and NADH-linked dehydrogenases, including beta-oxidationthe and segments of the TCA cycle.
N-junction on the pathway level of NADH-linked dehydrogenases, including the TCA cycle.
Q-junction on the pathway level of electron transfer complexes converging at the Q-junction (S and Gp).
Tm on the single step level of cytochrome c oxidase (CIV), the terminal step in the aerobic electron transfer-pathway. Tm can be included or excluded at the end of a SUIT protocol. To simplify the categorization, Tm is not considered in this system of SUIT protocols.

Single pathway type

ET-pathway-level 1: CIV

ET-pathway-level 3: S, CII-pathway to Q

ET-pathway-level 3: Gp, CGpDH-pathway to Q

ET-pathway-level 4: N, N-junction or CI-pathway to Q

ET-pathway-level 5: F, FAO, F-junction, CETF- supported by CI-pathway to Q

Multiple ET-pathway with FNSGp

Multiple ET pathways with NS

NS

FNS

NSGp

FNSGp

Multiple ET pathways with N (without S)

FN

NGp

FNGp

Multiple ET pathways without N

Addition of malate alone (M without P or G) is not considered as substrate type N. However, high mt-malic enzyme activity requires a change of this concept, when M alone represents an ET-pathway ccompetent substrate state. Low concentration of M may be used to support FAO, whereas a higher concentration of M may be required for N-junction respiratory capacity to override FAO capacity; this needs corresponding kinetic analyses (SUIT test protocols).

FS

FGp

SGp

FSGp

@@ Line 1: / Line 1: @@
 {{MitoPedia
-|abbr=SUITp-Catg
+|abbr=SUIT-catg
-|description='''Categories of SUIT protocols''' group '''SUIT protocols''' according to all [[substrate types]] involved in a protocol, independent of titrations of inhibitors which block the oxidation of the substrates present. ROX states may or may not be included in a SUIT protocol, which does not change its category.
+|description=[[File:SUIT-catg_MitoPathway types.jpg|right|200px]]
-|info=[[MiPNet21.06 SUIT reference assay]]
+'''Categories of SUIT protocols''' group [[MitoPedia: SUIT |SUIT protocols]] according to all substrate types involved in a protocol (F, N, S, Gp), independent of the sequence of titrations of substrates and inhibitors which define the [[Electron-transfer-pathway state]]s. The [[N-pathway control |N-type substrates]] are listed in parentheses, independent of the sequence of titrations. ROX states may or may not be included in a SUIT protocol, which does not change its category. Similarly, the [[CIV]] assay may or may not be added at the end of a SUIT protocol, without effect on the category of a SUIT protocol.
+* '''F''' - ET-pathway-level 5: [[FADH2 |FADH<sub>2</sub>]]-linked substrates (FAO) with obligatory support by the N-linked pathway.
+* '''N''' - ET-pathway-level 4: [[NADH]]-linked substrates (CI-linked).
+* '''S''' - ET-pathway-level 3: [[Succinate]] (CII-linked).
+* '''Gp''' - ET-pathway-level 3: [[Glycerophosphate]] (CGpDH-linked).
+* '''Y(X)'''- In the SUIT general protocols Y makes reference to the ET-pathway state and X to the combination os substrates added for the corresponding pathway.
+» [[#Categorization of SUIT protocols: ETS pathway control states |'''MiPNet article''']]
+|info=[[MiPNet21.06 SUIT RP]]
 }}
 {{MitoPedia concepts
-|mitopedia concept=MitoFit Quality Control System
+|mitopedia concept=SUIT concept
+}}
+__TOC__
+= Categories of SUIT protocols and ET-pathway control states =
+{{Publication
+|title=Gnaiger E (2017) Categories of SUIT protocols and ETS pathway control states. MiPNet 2017-03-12; original 2016-03-20; edited 2016-08-21.
+|info=[[MiPNet21.06 SUIT RP]]
+|authors=Oroboros
+|year=2017
+|journal=MiPNet
+|abstract=The complexity of SUIT protocols is primarily determined by the large number of [[Electron transfer-pathway state]]s and fuel substrates involved, compared to only three well defined [[coupling-control state]]s. Whereas the [[SUIT protocol names]] specify all sequential steps in a SUIT protocol, the categories of SUIT protocols reduce this diversity to a list of substrate types involved.
+|mipnetlab=AT Innsbruck Oroboros
 }}
-{{MitoPedia methods}}
+{{Labeling
-{{MitoPedia SUIT
+|area=Instruments;methods
-|mitopedia SUIT=SUIT protocol
+|pathways=F, N, S, Gp, CIV, NS, Other combinations, ROX
+|instruments=Theory
 }}
-{{MitoPedia topics}}
+[[File:SUIT-nomenclature.jpg|right|300px|SUIT protocols]]
-[[File:SUITp nomenclature.jpg|right|300px|SUIT protocols]]
-__TOC__
+== Towards a library of SUIT protocols ==
-== Categorization of SUIT protocols: substrate types ==
+:::: At the present stage of development of the [[MitoPedia:_SUIT#Library_of_SUIT_protocols |Library of SUIT protocols]] as part of the [[MitoFit Quality Control System]], the substrate types linked to five ET-pathway types are considered.
+::::* '''F-junction''' on the pathway level of converging FADH<sub>2</sub>- and NADH-linked dehydrogenases, including beta-oxidationthe and segments of the TCA cycle.
+::::* '''N-junction''' on the pathway level of NADH-linked dehydrogenases, including the TCA cycle.
+::::* '''Q-junction''' on the pathway level of electron transfer complexes converging at the [[Q-junction]] (S and Gp).
+::::* '''Tm''' on the single step level of cytochrome ''c'' oxidase (CIV), the terminal step in the aerobic electron transfer-pathway. Tm can be included or excluded at the end of a SUIT protocol. To simplify the categorization, Tm is not considered in this system of SUIT protocols.
-There are many ways to define groups of SUIT protocols. Since the complexity of SUIT protocols is primarily determined by the large number of possible [[substrate state]]s, and to a lesser extent by the smaller number of possible [[coupling state]]s, a relevant type of categories of SUIT protocols considers the substrate types involved. Whereas the [[SUIT protocol names]] include all specific substrates applied in the SUIT protocol, the categories of SUIT protocols reduce this diversity to [[substrate types]].
-At the present stage of development of the 'library of SUIT protocols' as part of the [[MitoFit Quality Control System]], five substrate types are considered:
+== Single pathway type ==
-* On the pathway level of converging NADH- and FADH<sub>2</sub>-linked dehydrogenases, including the TCA cycle and beta-oxidation:
-:'''N:''' [[NADH]]-linked substrates (CI-linked)
-:'''F:''' [[FADH2 |FADH<sub>2</sub>]]-linked substrates (FAO)
-* On the pathway level of electron transfer complexes converging at the Q-junction:
-:'''S:''' [[Succinate]] (CII-linked)
-:'''Gp:''' [[Glycerophosphate]] (CGpDH-linked)
-* On the single step level of cytochrome ''c'' oxidase (CIV), the terminal step in the aerobic electron transfer system:
-:'''Tm:''' Artificial electron transfer susbstrate [[TMPD]] (Tm) maintained in a reduced state by [[ascorbate]] (As) and reducing cytochrome ''c'' as the substrate of [[CIV]].
+=== ET-pathway-level 1: CIV ===
+[[File:SUIT-catg CIV.jpg|200px]]
-== SUITp-Catg: single substrate type ==
+=== ET-pathway-level 3: S, CII-pathway to Q ===
-[[File:SUITp-Catg NFSGpTm.jpg|left|200px]]
+[[File:SUIT-catg S.jpg|200px]]
-<br />
-:'''N''' - ETS-level 4
-:'''F''' - ETS-level 4
+=== ET-pathway-level 3: Gp, CGpDH-pathway to Q ===
+[[File:SUIT-catg Gp.jpg|200px]]
-:'''S''' - ETS-level 3
+=== ET-pathway-level 4: N, N-junction or CI-pathway to Q ===
+[[File:SUIT-catg N.jpg|200px]]
-:'''Gp''' - ETS-level 3
+=== ET-pathway-level 5: F, FAO, F-junction, CETF- supported by CI-pathway to Q ===
+[[File:SUIT-catg F.jpg|200px]]
-:'''Tm''' - ETS-level 1. Tm can always be included or excluded at the end of a SUIT protocol. To simplify the categorization, Tm is not considered in this system of SUIT protocols.
-<br />
+== Multiple ET-pathway with FNSGp ==
+[[File: SUIT-catg_FNSGpCIV.jpg|200px]]
-== SUITp-Catg: multiple substrate types with NS ==
+== Multiple ET pathways with NS ==
 === NS ===
-[[File:SUITp-Catg NS.jpg|200px]]
+[[File:SUIT-catg NS.jpg|200px]]
-=== NFS ===
+=== FNS ===
-[[File:SUITp-Catg NFS.jpg|200px]]
+[[File:SUIT-catg FNS.jpg|200px]]
 === NSGp ===
-[[File:SUITp-Catg NSGp.jpg|200px]]
+[[File:SUIT-catg NSGp.jpg|200px]]
-=== NFSGp ===
+=== FNSGp ===
-[[File:SUITp-Catg NFSGp.jpg|200px]]
+[[File:SUIT-catg FNSGp.jpg|200px]]
-== SUITp-Catg: multiple substrate types with N (without S) ==
+== Multiple ET pathways with N (without S) ==
-=== NF ===
+=== FN ===
-[[File:SUITp-Catg NF.jpg|200px]]
+[[File:SUIT-catg FN.jpg|200px]]
 === NGp ===
-[[File:SUITp-Catg NGp.jpg|200px]]
+[[File:SUIT-catg NGp.jpg|200px]]
-=== NFGp ===
+=== FNGp ===
-[[File:SUITp-Catg NFGp.jpg|200px]]
+[[File:SUIT-catg FNGp.jpg|200px]]
-== SUITp-Catg: multiple substrate types without N ==
+== Multiple ET pathways without N ==
-: F and S without N are problematic substrate states due to accumulation of Oxa or Acetyl-CoA. Therefore, addition of malate alone (M without P or G) is not considered as substrate type N. However, high mt-malic enzyme activity requires a change of this concept, when M alone represents an ETS ccompetent substrate state. Low concentration of M may be used to support FAO, whereas a higher concentration of M may be required for N-linked respiratory capacity to override FAO capacity; this needs corresponding kinetic analyses ([[SUIT test protocols]]).
+:::: Addition of malate alone (M without P or G) is not considered as substrate type N. However, high mt-malic enzyme activity requires a change of this concept, when M alone represents an ET-pathway ccompetent substrate state. Low concentration of M may be used to support FAO, whereas a higher concentration of M may be required for N-junction respiratory capacity to override FAO capacity; this needs corresponding kinetic analyses ([[SUIT test protocols]]).
 === FS ===
-[[File:SUITp-Catg FS.jpg|200px]]
+[[File:SUIT-catg FS.jpg|200px]]
 === FGp ===
-[[File:SUITp-Catg FGp.jpg|200px]]
+[[File:SUIT-catg FGp.jpg|200px]]
 === SGp ===
-[[File:SUITp-Catg SGp.jpg|200px]]
+[[File:SUIT-catg SGp.jpg|200px]]
 === FSGp ===
-[[File:SUITp-Catg FSGp.jpg|200px]]
+[[File:SUIT-catg FSGp.jpg|200px]]

Difference between revisions of "Categories of SUIT protocols"