| 1. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 2. |
- Havelius, Kajsa G. V., et al.
(författare)
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Metalloradical EPR Signals from the Y-Z center dot S-State Intermediates in Photosystem II
- 2010
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Ingår i: Applied Magnetic Resonance. - : Springer Science and Business Media LLC. - 0937-9347 .- 1613-7507. ; 37:1-4, s. 151-176
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Forskningsöversikt (refereegranskat)abstract
- The redox-active tyrosine residue (Y-Z) plays a crucial role in the mechanism of the water oxidation. Metalloradical electron paramagnetic resonance (EPR) signals reflecting the light-induced Y-Z center dot in magnetic interaction with the CaMn4-cluster in the particular S-state, Y-Z center dot S-X intermediates, have been found in intact photosystem II. These so-called split EPR signals are induced by illumination at cryogenic temperatures and provide means to both study the otherwise transient Y-Z center dot and to probe the S-states with EPR spectroscopy. The illumination used for signal induction grouped the observed split EPR signals in two categories: (i) Y-Z in the lower S-states was oxidized by P680(+) formed via charge separation, while (ii) Y-Z in the higher S-states was oxidized by an excited, highly oxidizing Mn species. Applied mechanistic studies of the Y-Z center dot S-X intermediates in the different S-states are reviewed and compared to investigations in photosystem II at physiological temperature. Addition of methanol induced S-state characteristic changes in the split signals' formation which reflect changes in the magnetic coupling within the CaMn4-cluster due to methanol binding. The pH titration of the split EPR signals, on the other hand, could probe the proton-coupled electron transfer properties of the Y-Z oxidation. The apparent pK (a)s found for decreased split signal induction were interpreted in the fate of the phenol proton.
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| 3. |
- Havelius, Kajsa G. V., et al.
(författare)
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The formation of the split EPR signal from the S-3 state of Photosystem II does not involve primary charge separation
- 2011
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Ingår i: Biochimica et Biophysica Acta - Bioenergetics. - : Elsevier BV. - 0005-2728 .- 1879-2650 .- 0006-3002 .- 1878-2434. ; 1807:1, s. 11-21
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Tidskriftsartikel (refereegranskat)abstract
- Metalloradical EPR signals have been found in intact Photosystem II at cryogenic temperatures. They reflect the light-driven formation of the tyrosine Z radical (Y-z(center dot)) in magnetic interaction with the CaMn4 cluster in a particular S state. These so-called split EPR signals, induced at cryogenic temperatures, provide means to study the otherwise transient Y-z(center dot) and to probe the S states with EPR spectroscopy. In the S-0 and S-1 states, the respective split signals are induced by illumination of the sample in the visible light range only. In the S-3 state the split EPR signal is induced irrespective of illumination wavelength within the entire 415-900 nm range (visible and near-IR region) [Su, J. H., Havelius, K. G. V., Ho, F. M., Han, G., Mamedov, F., and Styring, S. (2007) Biochemistry 46. 10703-10712]. An important question is whether a single mechanism can explain the induction of the Split S-3 signal across the entire wavelength range or whether wavelength-dependent mechanisms are required. In this paper we confirm that the Y-z(center dot) radical formation in the S-1 state, reflected in the Split S-1 signal, is driven by P680-centered charge separation. The situation in the S-3 state is different. In Photosystem II centers with pre-reduced quinone A (Q(A)), where the P680-centered charge separation is blocked, the Split S-3 EPR signal could still be induced in the majority of the Photosystem II centers using both visible and NIR (830 nm) light. This shows that P680-centered charge separation is not involved. The amount of oxidized electron donors and reduced electron acceptors (Q(A)(-)) was well correlated after visible light illumination at cryogenic temperatures in the S-1 state. This was not the case in the S-3 state, where the Split S-3 EPR signal was formed in the majority of the centers in a pathway other than P680-centered charge separation. Instead, we propose that one mechanism exists over the entire wavelength interval to drive the formation of the Split S-3 signal. The origin for this, probably involving excitation of one of the Mn ions in the CaMn4 cluster in Photosystem II, is discussed.
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| 4. |
- Ho, Felix M.
(författare)
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Structural and mechanistic investigations of photosystem II through computational methods
- 2012
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Ingår i: Biochimica et Biophysica Acta - Bioenergetics. - : Elsevier BV. - 0005-2728 .- 1879-2650. ; 1817:1, s. 106-120
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Forskningsöversikt (refereegranskat)abstract
- The advent of oxygenic photosynthesis through water oxidation by photosystem II (PSII) transformed the planet, ultimately allowing the evolution of aerobic respiration and an explosion of ecological diversity. The importance of this enzyme to life on Earth has ironically been paralleled by the elusiveness of a detailed understanding of its precise catalytic mechanism. Computational investigations have in recent years provided more and more insights into the structural and mechanistic details that underlie the workings of PSII. This review will present an overview of some of these studies, focusing on those that have aimed at elucidating the mechanism of water oxidation at the CaMn(4) cluster in PSII, and those exploring the features of the structure and dynamics of this enzyme that enable it to catalyse this energetically demanding reaction. This article is part of a Special Issue entitled: Photosystem II.
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| 5. |
- Linke, Katrin, et al.
(författare)
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Water in Photosystem II : Structural, functional and mechanistic considerations
- 2014
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Ingår i: Biochimica et Biophysica Acta - Bioenergetics. - : Elsevier BV. - 0005-2728 .- 1879-2650. ; 1837:1, s. 14-32
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Forskningsöversikt (refereegranskat)abstract
- Water is clearly important for the functioning of Photosystem II (PSII). Apart from being the very substrate that needs to be transported in this water oxidation enzyme, water is also vital for the transport of protons to and from the catalytic center as well as other important co-factors and key residues in the enzyme. The latest crystal structural data of PSII have enabled detailed analyses of the location and possible function of water molecules in the enzyme. Significant progress has also been made recently in the investigation of channels and pathways, through the protein complex. Through these studies, the mechanistic significance of water for PSII is becoming increasingly clear. An overview and discussion of key aspects of the current research on water in PSII is presented here. The role of water in three other systems (aquaporin, bacteriorhodopsin and cytochrome P450) is also outlined to illustrate further points concerning the central significance that water can have, and potential applications of these ideas for continued research on PSII. It is advocated that water be seen as an integral part of the protein and far from a mere solvent.
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| 6. |
- Magnuson, Ann, et al.
(författare)
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Modeling Photosystem I with the alternative reaction center protein PsaB2 in the nitrogen fixing cyanobacterium Nostoc punctiforme
- 2011
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Ingår i: Biochimica et Biophysica Acta - Bioenergetics. - : Elsevier BV. - 0005-2728 .- 1879-2650. ; 1807:9, s. 1152-1161
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Tidskriftsartikel (refereegranskat)abstract
- Five nitrogen fixing cyanobacterial strains have been found to contain PsaB2, an additional and divergent gene copy for the Photosystem I reaction center protein PsaB. In all five species the divergent gene, psaB2, is located separately from the normal psaAB operon in the genome. The protein, PsaB2, was recently identified in heterocysts of Nostoc punctiforme sp. strain PCC 73102. 12 conserved amino acid replacements and one insertion, were identified by a multiple sequence alignment of several PsaB2 and PsaB1 sequences. Several, including an inserted glutamine, are located close to the iron-sulfur cluster F(x) in the electron transfer chain. By homology modeling, using the Photosystem I crystal structure as template, we have found that the amino acid composition in PsaB2 will introduce changes in critical parts of the Photosystem I protein structure. The changes are close to F(x) and the phylloquinone (PhQ) in the B-branch, indicating that the electron transfer properties most likely will be affected. We suggest that the divergent PsaB2 protein produces an alternative Photosystem I reaction center with different structural and electron transfer properties. Some interesting physiologcial consequences that this can have for the function of Photosystem I in heterocysts, are discussed.
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| 7. |
- Sjöholm, Johannes, et al.
(författare)
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Visible light induction of an EPR split signal in photosystem II in the S2 state reveals the importance of charges in the oxygen evolving center during catalysis : a unifying model
- 2012
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Ingår i: Biochemistry. - : American Chemical Society (ACS). - 0006-2960 .- 1520-4995. ; 51:10, s. 2054-2064
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Tidskriftsartikel (refereegranskat)abstract
- Cryogenic illumination of Photosystem II (PSII) can lead to the trapping of the metastable radical Y-z(center dot), the radical form of the redox-active tyrosine residue D1-Tyr161 (known as Y-z). Magnetic interaction between this radical and the CaMn4 cluster of PSII gives rise to so-called split electron paramagnetic resonance (EPR) signals with characteristics that are dependent on the S state. We report here the observation and characterization of a split EPR signal that can be directly induced from PSII centers in the S-2 state through visible light illumination at 10 K. We further show that the induction of this split signal takes place via a Mn-centered mechanism, in the same way as when using near-infrared light illumination [Koulougliotis, D., et al. (2003) Biochemistry 42, 3045-3053]. On the basis of interpretations of these results, and in combination with literature data for other split signals induced under a variety of conditions (temperature and light quality), we propose a unified model for the mechanisms of split signal induction across the four S states (S-0, S-1, S-2, and S-3). At the heart of this model is the stability or instability of the Y-z(center dot)(D1-His190)(+) pair that would be formed during cryogenic oxidation of Y-Z. Furthermore, the model is closely related to the sequence of transfers of protons and electrons from the CaMn4, cluster during the S cycle and further demonstrates the utility of the split signals in probing the immediate environment of the oxygen-evolving center in PSII.
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| 8. |
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