6. Gene Families Involved in Cellular Dynamics

  1. Prof. Dr. Horst Feldmann1,2

Published Online: 26 SEP 2012

DOI: 10.1002/9783527659180.ch6

Yeast: Molecular and Cell Biology, Second Edition

Yeast: Molecular and Cell Biology, Second Edition

How to Cite

Feldmann, H. (ed) (2012) Gene Families Involved in Cellular Dynamics, in Yeast: Molecular and Cell Biology, Second Edition, Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany. doi: 10.1002/9783527659180.ch6

Editor Information

  1. 1

    Adolf Butenandt Institute, Molecular Biology, Ludwig-Maximilians-Universität M¨nchen, Schillerstr. 44, 80336 M¨nchen, Germany

  2. 2

    Ludwig-Thoma-Strasse 22B, 85232 Bergkirchen, Germany

Publication History

  1. Published Online: 26 SEP 2012
  2. Published Print: 22 AUG 2012

ISBN Information

Print ISBN: 9783527332526

Online ISBN: 9783527659180

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Keywords:

  • genefamilies;
  • cellular dynamics;
  • ATP-/GTP-binding proteins;
  • regulatory ATPases;
  • protein modification

Summary

• Every task in a cell consumes energy in the form of ATP. Therefore, a cell's survival depends on the supply of sufficient ATP. Even cells incapable of active movement within their environment have to perform essential intracellular motility processes. As we have learned in previous chapters, a variety of mechanisms have evolved that generate the mechanical forces required to drive the intracellular movement of biomolecules or even of whole organelles. A particularly successful and ubiquitous mode of biological force production utilizes the motor proteins we have described in Chapter 2. All anabolic reactions mentioned in Chapter 3 in one or the other biosynthetic step depend on enzymes that convert the energy gained from the hydrolysis of ATP into new chemical bonds. This is particularly evident in the processes of DNA replication, DNA transcription, or protein biosynthesis by ribosomes. Subtle movements of macromolecular structures occur during chromatin remodeling, mostly powered by the consumption of ATP.

• This chapter presents some yeast gene families that contribute to cellular dynamics. In many cases, the products of single members of these families share characteristic structural and/or functional features. In Section 6.1, specialized ATP- and GTP-binding proteins are considered. Among these, the H+-transporting and ion-transporting ATPases deserve particular mention. Next, a large group of proteins with similar functions – the chaperones (also called heat-shock proteins) – are detailed. They will show up in many contexts in all further chapters, as they are responsible for the folding of nascent peptides, refolding of “damaged” proteins, or preventing denaturation of correctly folded proteins (“antistress chaperones”). The listing includes some extraordinary members of this family.

• Of outstanding importance for intracellular dynamics are the small GTPases (RAS superfamily), which according to their specialization can be grouped into subfamilies, like the Ras family proper, known from their activities in Ras–cAMP signaling; the Rho family, the members of which are involved in the establishment and maintenance of cell polarity as well as in the organization of the cell skeleton and cell integrity; the Rab family, comprising small GTPases mainly designed for mediating vesicular transport; and finally the ARF family, whose members serve in the formation of coated vesicles and in other aspects of intracellular traffic. An extra group in the superfamily is represent by the small nuclear GTPase, Ran, and its associates, whose prominent function is to regulate nuclear traffic and the exchange of molecules through the nuclear pores in both directions. In this context, the tripartite G-proteins sensing or mediating cellular signaling are also considered.

• In recent years, the superfamily of “ATPases associated with diverse cellular activities” (AAA+ proteins) has grown enormously. In fact, these proteins share (one or two) specialized ATPase domain(s) that are combined with other functional domains, so that members of this family can participate in diverse cellular processes, such as (i) controlling the fate of proteins variously facilitating protein folding and unfolding, (ii) the assembly and disassembly of protein complexes, (iii) protein transport through membrane fusion, (iv) programmed protein degradation (proteolysis, cell cycle control), and (v) remodeling of chromatin.

• One particular group of the AAA proteins, six subunits of the regulatory particle of the eukaryotic 26S proteasome, contribute a unique tool for programmed proteolysis in the UPS. Before the proteasome can become active, proteins to be degraded have to be marked by specific signals, namely by combining them with target moieties, such as ubiquitin or ubiquitin-like entities – a process that needs specific enzymes and consumes energy. As we know today, this process has evolved into so many facets that the system has been adapted to very distinctive and specialized functions. Not only are proteins labeled by ubiquitin or ubiquitin-like modifications to undergo programmed proteolysis, but this type of labeling is also utilized as a suitable tag to direct proteins to their cognate destinations in cellular traffic. The structure and function of the proteasomal constituents are discussed in some detail, as well as regulatory aspects of proteasome activity.

• A further section is devoted to the problem of how “simple” chemical modifications of proteins contribute to alter their behavior, function, or cellular localization. This alludes to the general regulatory principle of protein phosphorylation and dephosphorylation. Since protein kinases and protein phosphatases will reappear in so many contexts, we restrict the presentation of these enzymes in yeast to a more or less tabular form.

• The final section presents a survey on yeast helicases. First, we list all putative members of the helicase superfamily occurring in yeast, followed by elaborate descriptions of RNA helicases involved in various cellular processes, as well as accounting the delicate (and mostly regulatory) functions of DNA helicases. These portraits are also meant to refine the description of helicases given in previous chapters and offer a summary of the current views.