Molecular Anatomy of Cellular Systems (eBook)

I. Endo, T. Kudo, H. Osada, T. Shibata, I. Yamaguchi (Herausgeber)

eBook Download: EPUB

2002 | 1. Auflage
240 Seiten
Elsevier Science (Verlag)
978-0-08-053674-3 (ISBN)

Infos

In this book, the progress during the last ten years is reviewed and future plans outlined to realize and establish the concept of design in the biological sciences.

Design is a leading concept as well as the principal motivation for the creation of artificial systems. A successful design generally requires that the structures and functions of the elements that constitute the system as well as the principles that determine how the elements cooperate together to create function be fully understood. These requirements have not been satisfied within the fields of biotechnology and medicine. Compared to the recent emergence of artificial systems, living organisms acquired their present day structures and functions through evolution over three to four billion years. Despite the fact that the design of living organisms is recorded in the DNA sequence, our understanding of the structures and functions of the elements that constitute living organisms is very limited.

To fulfill the requirements, the following approaches were initiated under a ten-year project entitled 'Biodesign Research'. Firstly, we tried to isolate and characterize the functional elements that constitute the organelles of various organisms. Secondly, we tried to reconstitute systems that reproduce biological functions in vitro from individual elements in order to understand how the elements cooperate together to yield a function. Thirdly, we attempted to resolve biological structures at various resolutions ranging from the atomic to the cellular level to further our knowledge about the fundamental principles that various functions at the molecular level and to design artificial systems.

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In this book, the progress during the last ten years is reviewed and future plans outlined to realize and establish the concept of design in the biological sciences. Design is a leading concept as well as the principal motivation for the creation of artificial systems. A successful design generally requires that the structures and functions of the elements that constitute the system as well as the principles that determine how the elements cooperate together to create function be fully understood. These requirements have not been satisfied within the fields of biotechnology and medicine. Compared to the recent emergence of artificial systems, living organisms acquired their present day structures and functions through evolution over three to four billion years. Despite the fact that the design of living organisms is recorded in the DNA sequence, our understanding of the structures and functions of the elements that constitute living organisms is very limited. To fulfill the requirements, the following approaches were initiated under a ten-year project entitled "e;Biodesign Research"e;. Firstly, we tried to isolate and characterize the functional elements that constitute the organelles of various organisms. Secondly, we tried to reconstitute systems that reproduce biological functions in vitro from individual elements in order to understand how the elements cooperate together to yield a function. Thirdly, we attempted to resolve biological structures at various resolutions ranging from the atomic to the cellular level to further our knowledge about the fundamental principles that various functions at the molecular level and to design artificial systems.

Inhalt

Front Cover 1
MOLECULAR ANATOMY OF CELLULAR SYSTEMS 4
Copyright Page 5
CONTENTS 8
PREFACE 6
PART I: CELLULAR FUNCTIONS 10
Chapter 1. Stress meets development in p38 MAP kinase 12
Chapter 2. Molecular dissection of cytotoxic functions mediated by T cells 22
Chapter 3. Molecular imaging of the cytoskeleton using GFP-actin fluorescence microscopy 34
Chapter 4. Golgi-acting drugs: inducers and inhibitors of Golgi dispersal as probes to analyze Golgi membrane dynamics 44
Chapter 5. Regulation of protein sorting and trafficking between the endoplasmic reticulum and the Golgi apparatus in yeast 54
Chapter 6. An unexpected gift from fungicide metabolism studies: blasticidin S deaminase (BSD) from Aspergillus terreus 64
Chapter 7. Isolation and analysis of genes from phytopathogenic fungi 70
Chapter 8. A novel type of Na+/H+ antiporter: its unique characteristics and function 84
PART II: NUCLEAR FUNCTIONS 94
Chapter 9. Genetic analysis of the genes involved in mitosis in fission yeast Schizosaccharomyces pombe 96
Chapter 10. Intergenomic transcriptional interplays between plastid as a cyanobacterial symbiont and nucleus 114
Chapter 11. From viral RNA genome to infectious ribonucleoprotein complexes through RNA replication 130
Chapter 12. Mechanisms of regulation of eukaryotic homologous DNA recombination 150
PART III: PROTEIN FUNCTIONS 166
Chapter 13. Studies on photoreactive enzyme --nitrile hydratase-- 168
Chapter 14. Structural and functional analyses of proteins involved in translation, DNA recombination, chromosome architecture, and signal transduction 178
Chapter 15. The importance of the hydrophobic pocket in actin subdomain 4 for Ca2+-activation of actin-activated myosin ATPase in the presence of Tropomyosin-Troponin 190
Chapter 16. Physiological functions and molecular structures of new types of hemoproteins 198
Chapter 17. Unity and diversity in biological oxidation 214
Index of authors 230
Index of key words 232

Textauszug

Stress meets development in p38 MAP kinase

Tatsuhiko Sudoa,*; Masumi Maruyamaa; Hiroyuki Osadaa    a Antibiotics Laboratory, RIKEN, 2-1 Hirosawa Wako Saitama 351-0198, Japan
* Our works on p38 MAPK have been supported by Biodesign Research Program, President’s Special Research Grant and Bioarchitect Research Project of RIKEN. email address: [e-mail]

p38 mitogen-activated protein kinases (MAPKs) form one of three major families of MAPKs and play various roles in converting extracellular stimuli into cellular responses. In the past years, extensive and intensive studies highlighted their roles in the stress responses, such as osmotic shock, UV irradiation and inflammatory cytokines. Recent genetic studies reveal their additional functions in development. This review aims to provide an overview of their functions update for better understandings of physiological and developmental roles of p38(s) and for the future development of therapeutic reagents controlling p38 signal transduction pathways.

1 INTRODUCTION

A large body of knowledge has been accumulated in the last decade regarding the signaling pathways converting extracellular stimuli through MAPKs into specific cellular responses (1–4). The MAPKs represented by extracellular signal regulated kinase (ERK), c- Jun N-terminal kinase (JNK) and p38 MAPK are one of the best characterized groups of the protein kinases and play crucial roles in the determination and execution of the cell fate leading to proliferation, differentiation and cell death. These kinases have a common feature that they are phosphorylated and activated by specific upstream kinases, MAP kinase kinase/ MAPK upstream activating kinase (MKK/MEK), and then transmit signals to the downstream target proteins by phosphorylating serine or threonine residue(s) (5–7). A prototype of the multistep phospho-relay system can be already observed in yeast and evolutionary conserved to flies and human in more complex fashions (8–11). Among them, ERK pathway is best characterized and plays a major role in converting mitogenic stimuli into cellular responses (12). JNK is a central component of the JNK pathway and was first identified as an upstream kinase for c-Jun, a major component of AP-1 transcription factors (13,14). The transcription factor as well as ATF2/CRE-BP1 is activated by phosphorylation and regulate many gene expressions (15). The newest member of the MAPK family, p38, was simultaneously identified as a cytokine suppressive antiinflammatory drug (CSAID)-binding protein (16), a lipopolysaccharide (LPS)-activated kinase (17) or a stress-responsive kinase (18). p38 also plays a central role in the p38 pathway. Since latter two kinases are activated in response to the environmental stress such as UV irradiation, heat, osmotic shock, genotoxic reagents, proinflammatory cytokines and protein synthesis inhibitors, they are also categorized as stress-activated protein kinases (SAPKs). Even though each pathway has unique regulatory features, the stress stimuli often result in their activation simultaneously.

In the past years, the functional analyses of the p38 have been accelerated by the discovery and availability of the p38 specific inhibitors, such as SB202190 (16) and SB203580 (19). So far, four isoforms (α, β, γ, δ) of p38 have been cloned and characterized in mammals (16–18, 20–24), and only p38α and p38β are sensitive to these inhibitors (25). These new tools together with advanced genetic techniques, such as productions of transgenic flies and mice, facilitated functional studies of p38 not only in physiology but also in development.

This review focuses on the functions of p38 upon environmental stress and also include some of the recent genetic studies showing developmental functions of p38.

2 p38 MAP KINASE FAMILY

2.1 Members

p38α (originally named p38) was identified as a CSAID-binding protein, a LPS-activated kinase or a stress-responsive kinase. So far, four isoforms (α, β, γ, δ) of p38 have been cloned and characterized in mammals (16-18, 20-24, Table 1). They have at least 60 % homology between each of their amino acid sequences. One for yeast (8) and two for flies (26–28) had been also identified as functional homologues for p38. The identity is still high at more than 50 % between yeast high osmolarity glycerol (Hog1) gene product and human p38. Even though four members of mammalian p38s have high homology in their amino acid sequences, p38α and p38β form a subgroup based on their sensitivities to SB203580 (25). p38α and p38β show relatively broad mRNA expression profiles in human tissues (29). On the other hand p38γ and p38δ have prominent or rather restricted expression profiles in skeletal muscle, and kidney and lung respectively (20). As a common feature for p38s, they all have threonine-glycine-tyrosine (TGY) motif in their activation loops. Both threonine and tyrosine residues are phosphorylated leading to the activation of p38 (30, 31). Once p38s were phosphorylated and activated by the specific upstream kinases, then transmit these signals to the down stream targets by phosphorylating serine or threonine residue(s) followed by proline. This characteristic can be also observed in cell cycle regulated kinases, such as cdc2, to be classified as proline-directed kinases (32).

Table 1

Characteristics of human p38 MAPK isoforms

p38 (α)

MKK3, 4, 6

Broad

+

p38β

MKK6

Broad

+

p38γ

MKK3, 6

Skeletal muscle

-

p38δ

MKK3, 6

Kidney and lung

-

2.2 Regulations

Evolutionary conserved p38 pathways from yeast to mammals were governed by similar mechanisms. Hog1 gene product, a homologue of p38 in budding yeast, is phosphorylated and activated by PBS2 (9), the yeast homologue of MKK, in response to the high osmolarity and p38 can functionally complement Hog1 deficient yeast strain in hyperosmotic conditions (33). In mammalian cells, upstream kinases such as MKK3, MKK6 and in some cases MKK4 phosphorylate and activate p38s with different spectra. That is MKK6 phosphorylates all members of p38 MAPKs but MKK3 can’t phosphorylate p38β (30). In addition to their activation by upstream kinases, the involvement of p62, first identified as a phosphorylation independent ligand of p56lck, in the regulation of p38 activity with a substrate dependent manner in vitro is recently proposed (34). The novel mechanism of the regulation of p38 activity somehow helps to clarify how various environmental stimuli exert different responses in cell type and/or in stimulation dependent fashions by using a limited number of signal transducers.

2.3 Targets

To date, many downstream targets for p38 have been described. These include transcription factors, such as ATF2 (18), MEF2C (35), CHOP (36), C/EBPβ (37), c-Jun (38) and so on. As mentioned above, c-Jun is phosphorylated in the activation domain by JNK (13). The phosphorylated residue(s) by p38 seemed to be different from the ones by JNK, suggesting the organized regulations of its transcriptional activity by different members of the closely related kinases (38). Other than transcription factors, cytoplasmic proteins represented by MAPKAPK2/3 (39, 40), MNK1/2 (41, 42) and MBP are also phosphorylated by p38. Among them, a functional relevance of the phosphorylation in vivo by p38 is well characterized with MAPKAPK2. MAPKAPK2 is phosphorylated and activated by p38 to phosphorylate HSP27 to regulate actin dynamics in cells (43). Moreover MAPKAPK2 is shown to be involved in the p38 regulation through controlling subcellular localizations (44).

2.4 Specific inhibitors

Recent discovery of p38 MAPKs specific inhibitors accelerate the functional analyses both in vivo and in vitro. Several p38 specific inhibitors are currently used in various approaches for our understandings of p38s. A series of pyridinyl imidazole compounds, represented by SB202190 and SB 203580, is originally identified by their abilities to suppress the production of inflammatory cytokines (Fig. 1). Then, this class of compounds has shown to specifically inhibit p38α and p38β activities by binding to their ATP pockets but not those of p38γ nor p38δ (25). This specificity is explained by the amino acid alignments at the back of ATP pockets, namely amino acid 106 to 108 (Thr-His-Leu) confer their strong competitivebinding affinities only for p38α and p38β, but not for p38γ and p38δ (45–47). The developments of specific inhibitors and/or activators for different isoforms of p38 will be the key toward the next step to assign their functions precisely.

Figure 1 Chemical structures of p38 MAPK inhibitors

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Produkt-Details

• Erscheint lt. Verlag: 20.8.2002
• Sprache: englisch
• Themenwelt: Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie
• Themenwelt: Naturwissenschaften ► Biologie ► Zellbiologie
• Themenwelt: Technik ► Umwelttechnik / Biotechnologie
• ISBN-10: 0-08-053674-3 / 0080536743
• ISBN-13: 978-0-08-053674-3 / 9780080536743