A question of size: the eukaryotic proteome and the problems in defining it

We discuss the problems in defining the extent of the proteomes for completely sequenced eukaryotic organisms (i.e. the total number of protein-coding sequences), focusing on yeast, worm, fly and human. (i) Six years after completion of its genome sequence, the true size of the yeast proteome is still not defined. New small genes are still being discovered, and a large number of existing annotations are being called into question, with these questionable ORFs (qORFs) comprising up to one-fifth of the ‘current’ proteome. We discuss these in the context of an ideal genome-annotation strategy that considers the proteome as a rigorously defined subset of all possible coding sequences (‘the orfome’). (ii) Despite the greater apparent complexity of the fly (more cells, more complex physiology, longer lifespan), the nematode worm appears to have more genes. To explain this, we compare the annotated proteomes of worm and fly, relating to both genome-annotation and genome evolution issues. (iii) The unexpectedly small size of the gene complement estimated for the complete human genome provoked much public debate about the nature of biological complexity. However, in the first instance, for the human genome, the relationship between gene number and proteome size is far from simple. We survey the current estimates for the numbers of human genes and, from this, we estimate a range for the size of the human proteome. The determination of this is substantially hampered by the unknown extent of the cohort of pseudogenes (‘dead’ genes), in combination with the prevalence of alternative splicing. (Further information relating to yeast is available at http://genecensus.org/yeast/orfome)     

Inositol pyrophosphates are required for DNA hyperrecombination in protein kinase c1 mutant yeast

Diphosphoinositol pentakisphosphate (InsP(7)) and bis-diphosphoinositol tetrakisphosphate (InsP(8)) contain energetic pyrophosphate groups, occur throughout animal and plant kingdoms, and are synthesized by a recently cloned family of inositol hexakisphosphate kinases (InsP(6)Ks). We report that these inositol pyrophosphates mediate homologous DNA recombination in yeast S. cerevisae. Hyperrecombination, caused by altered protein kinase C1 (PKC1), is lost in yeast with deletion of yeast InsP(6)K (yInsP(6)K) and can be restored selectively by catalytically active yeast or mammalian InsP(6)Ks. Inositol pyrophosphates are required for two forms of hyperrecombination that differ in mechanism, suggesting some generalities for actions of inositol pyrophosphates in recombination.     

Dexras1: a G protein specifically coupled to neuronal nitric oxide synthase via CAPON

Because nitric oxide (NO) is a highly reactive signaling molecule, chemical inactivation by reaction with oxygen, superoxide, and glutathione competes with specific interactions with target proteins. NO signaling may be enhanced by adaptor proteins that couple neuronal NO synthase (nNOS) to specific target proteins. Here we identify a selective interaction of the nNOS adaptor protein CAPON with Dexras1, a brain-enriched member of the Ras family of small monomeric G proteins. We find that Dexras1 is activated by NO donors as well as by NMDA receptor-stimulated NO synthesis in cortical neurons. The importance of Dexras1 as a physiologic target of nNOS is established by the selective decrease of Dexras1 activation, but not H-Ras or four other Ras family members, in the brains of mice harboring a targeted genomic deletion of nNOS (nNOS-/-). We also find that nNOS, CAPON, and Dexras1 form a ternary complex that enhances the ability of nNOS to activate Dexras1. These findings identify Dexras1 as a novel physiologic NO effector and suggest that anchoring of nNOS to specific targets is a mechanism by which NO signaling is enhanced.     

TRIPLES: a database of gene function in Saccharomyces cerevisiae

Using a novel multipurpose mini-transposon, we have generated a collection of defined mutant alleles for the analysis of disruption phenotypes, protein localization, and gene expression in Saccharomyces cerevisiae. To catalog this unique data set, we have developed TRIPLES, a Web-accessible database of TRansposon-Insertion Phenotypes, Localization and Expression in Saccharomyces. Encompassing over 250 000 data points, TRIPLES provides convenient access to information from nearly 7800 transposon-mutagenized yeast strains; within TRIPLES, complete data reports of each strain may be viewed in table format, or if desired, downloaded as tab-delimited text files. Each report contains external links to corresponding entries within the Saccharomyces Genome Database and International Nucleic Acid Sequence Data Library (GenBank). Unlike other yeast databases, TRIPLES also provides on-line order forms linked to each clone report; users may immediately request any desired strain free-of-charge by submitting a completed form. In addition to presenting a wealth of information for over 2300 open reading frames, TRIPLES constitutes an important medium for the distribution of useful reagents throughout the yeast scientific community. Maintained by the Yale Genome Analysis Center, TRIPLES may be accessed at http://ycmi.med.yale.edu/ygac/triples.htm     

A mammalian iron ATPase induced by iron

While molecular mechanisms for iron entry and storage within cells have been elucidated, no system to mediate iron efflux has been heretofore identified. We now describe an ATP requiring iron transporter in mammalian cells. (55)Fe is transported into microsomal vesicles in a Mg-ATP-dependent fashion. The transporter is specific for ferrous iron, is temperature- and time-dependent, and detected only with hydrolyzable nucleotides. It differs from all known ATPases and appears to be a P-type ATPase. The Fe-ATPase is localized together with heme oxygenase-1 to microsomal membranes with both proteins greatly enriched in the spleen. Iron treatment markedly induces ATP-dependent iron transport in RAW 264.7 macrophage cells with an initial phase that is resistant to cycloheximide and actinomycin D and a later phase that is inhibited by these agents. Iron release, elicited in intact rats by glycerol-induced rhabdomyolysis, induces ATP-dependent iron transport in the kidney. Mice with genomic deletion of heme oxygenase-1 have selective tissue iron accumulation and display augmented ATP-dependent iron transport in those tissues that accumulate iron.     

Tissue steroid sulfatase levels, testosterone and blood pressure

The objective of this study was to examine the response of tissue steroid sulfatase (STS) levels in hypertensive rat strains, when blood pressure (BP) was lowered by different techniques at an early age. A 4×3 factoral design was used, in which males (n=6–8) from four rat strains (WKY, SHR, SHR/a, SHR/y) at 4 weeks of age, were randomly assigned to one of three treatment groups: a hydralazine group, a castration group and a control group. BP was measured by the tail cuff technique and verified by tail catheter at the end of the experiment. BP was significantly reduced by both treatments in the hypertensive strains (SHR, SHR/a, SHR/y) compared to respective control groups. At 15–17 weeks of age, animals were euthanized and heart, kidney, adrenal glands and liver were assayed for STS levels. The major trend in tissue STS was that castration significantly lowered: adrenal, heart and liver STS in specific strains. In conclusion, castration and hydralazine significantly lowered the BP in the hypertensive rat strains, but only castration consistently lowered STS levels across strains implicating testosterone as a regulator of tissue STS.