Function Of Human Proteins Research Articles

Correspondence of function and phylogeny of ABC proteins based on an automated analysis of 20 model protein data sets

Using our BLAST-based procedure RiPE (Retrieval-induced Phylogeny Environment), which automates the evolutionary analysis of a protein family, we assembled a set of 1138 ABC protein components [adenosine triphosphate (ATP)-binding cassette and transmembrane domain] from the protein data sets of 20 model organisms and subjected them to phylogenetic and functional analysis. For maximum speed, we based the alignment directly on a homology search with a profile of all known human ABC proteins and used neighbor-joining tree estimation. All but 11 sequences from Homo sapiens, Arabidopsis thaliana, Drosophila melanogaster, and Saccharomyces cerevisiae were placed into the correct subtree/subfamily, reproducing published classifications of the individual organisms. By following a simple "function transfer rule", our comparative phylogenetic analysis successfully predicted the known function of human ABC proteins in 19 of 22 cases. Three functional predictions did not correspond, and 10 were novel. Predictions based on BLAST alone were inferior in five cases and superior in two. Bacterial sequences were placed close to the root of most subtrees. This placement coincides with domain architecture, suggesting an early diversification of the ABC family before the kingdoms split apart. Our approach can, in principle, be used to annotate any protein family of any organism included in the study.

Evolutionarily Conserved and Nonconserved Cellular Localizations and Functions of Human SIRT Proteins

Sir2 is a NAD+-dependent protein deacetylase that extends lifespan in yeast and worms. This study examines seven human proteins homologous to Sir2 (SIRT1 through SIRT7) for cellular localization, expression profiles, protein deacetylation activity, and effects on human cell lifespan. We found that: 1) three nuclear SIRT proteins (SIRT1, SIRT6, and SIRT7) show different subnuclear localizations: SIRT6 and SIRT7 are associated with heterochromatic regions and nucleoli, respectively, where yeast Sir2 functions; 2) SIRT3, SIRT4, and SIRT5 are localized in mitochondria, an organelle that links aging and energy metabolism; 3) cellular p53 is a major in vivo substrate of SIRT1 deacetylase, but not the other six SIRT proteins; 4) SIRT1, but not the other two nuclear SIRT proteins, shows an in vitro deacetylase activity on histone H4 and p53 peptides; and 5) overexpression of any one of the seven SIRT proteins does not extend cellular replicative lifespan in normal human fibroblasts or prostate epithelial cells. This study supports the notion that multiple human SIRT proteins have evolutionarily conserved and nonconserved functions at different cellular locations and reveals that the lifespan of normal human cells, in contrast to that of lower eukaryotes, cannot be manipulated by increased expression of a single SIRT protein.

Annotating the Human Proteome

The completion of the human genome has shifted the attention from deciphering the sequence to the identification and characterization of the encoded components. The identification and functional annotation of the proteome is here of special interest and starts with the identification of genes and transcripts as a prerequisite of proteome annotation. Gene predictions are very powerful in predicting most of the exons in a genome, but reliable gene structure predictions of both known and novel genes are dependent on existing transcript and protein information. An enormous amount of data already exists on the function of many human proteins, but this is scattered over many resources. Public domain databases are required to manage and collate this information and present it to the user community in both a human and machine readable manner.

Identification of a stanniocalcin paralog, stanniocalcin-2, in fish and the paracrine actions of stanniocalcin-2 in the mammalian ovary.

Stanniocalcin is a glycoprotein hormone important in the maintenance of calcium and phosphate homeostasis in fish. Two related mammalian stanniocalcin genes, STC1 and STC2, were found to be expressed in various tissues as paracrine regulators. We have demonstrated the existence of a second stanniocalcin gene in fish, designated fish STC2, with only 30% identity to fish STC1. However, phylogenetic analysis and comparison of the genomic structure of STC genes in vertebrates indicated that STC1 and STC2 genes were probably derived from a common ancestor gene. Based on the prominent expression of mammalian STC1 in the ovary, we tested STC2 expression in rat ovary and the regulation of STC2 expression by gonadotropins. Treatment of immature rats with pregnant mare serum gonadotropin increased STC2 transcripts, whereas subsequent treatment with human chorionic gonadotropin suppressed STC2 expression. Real-time PCR analyses also demonstrated that STC2 is expressed mainly in thecal layers. In situ hybridization studies also revealed that STC2 is expressed in thecal cell layers of antral and preovulatory follicles after gonadotropin stimulation. To elucidate the physiological functions of STC2, recombinant human and fish STC2 proteins were generated and found to be N-glycosylated homodimers. In cultured granulosa cells, treatment with human or fish STC2 suppressed FSH-induced progesterone, but not estradiol or cAMP, production. The STC2 suppression of progesterone production was associated with the inhibition of FSH-induced CYP11A and 3beta-hydroxysteroid dehydrogenase expression. Thus, STC2 is a functional homodimeric glycoprotein, and thecal cell-derived STC2 could play a paracrine role during follicular development.

Structure and function of human Vps20 and Snf7 proteins.

Snf7p (sucrose non-fermenting) and Vps20p (vacuolar protein-sorting) are small coil-coiled proteins involved in yeast MVB (multivesicular body) structure, formation and function. In the present study, we report the identification of three human homologues of yeast Snf7p, designated hSnf7-1, hSnf7-2 and hSnf7-3, and a single human Vps20p homologue, designated hVps20, that may have similar roles in humans. Immunofluorescence studies showed that hSnf7-1 and hSnf7-3 localized in large vesicular structures that also co-localized with late endosomal/lysosomal structures induced by overexpressing an ATPase-defective Vps4-A mutant. In contrast, overexpressed hVps20 showed a typical endosomal membrane-staining pattern, and co-expression of hVps20 with Snf7-1 dispersed the large Snf7-staining vesicles. Interestingly, overexpression of both hSnf7 and hVps20 proteins induced a post-endosomal defect in cholesterol sorting. To explore possible protein-protein interactions involving hSnf7 proteins, we used information from yeast genomic studies showing that yeast Snf7p can interact with proteins involved in MVB function. Using a glutathione S-transferase-capture approach with several mammalian homologues of such yeast Snf7p-interacting proteins, we found that all three hSnf7s interacted with mouse AIP1 [ALG-2 (apoptosis-linked gene 2) interacting protein 1], a mammalian Bro1p [BCK1 (bypass of C kinase)-like resistance to osmotic shock]-containing protein involved in cellular vacuolization and apoptosis. Whereas mapping experiments showed that the N-terminus of AIP1 containing both a Bro1 and an alpha-helical domain were required for interaction with hSnf7-1, Snf7-1 did not interact with another human Bro1-containing molecule, rhophilin-2. Co-immunoprecipitation experiments confirmed the in vivo interaction of hSnf7-1 and AIP1. Additional immunofluorescence experiments showed that hSnf7-1 recruited cytosolic AIP1 to the Snf7-induced vacuolar-like structures. Together these results suggest that mammalian Vps20, AIP1 and Snf7 proteins, like their yeast counterparts, play roles in MVB function.

A first-draft human protein-interaction map

Using data from model organisms, the authors have generated a large-scale human protein-protein interaction map. The map can be used to predict the function of human proteins.

Characterization of Functional Domains of Human EB1 Family Proteins

EB1 family proteins are evolutionarily conserved proteins that bind microtubule plus-ends and centrosomes and regulate the dynamics and organization of microtubules. Human EB1 family proteins, which include EB1, EBF3, and RP1, also associate with the tumor suppressor protein adenomatous polyposis coli (APC) and p150glued, a component of the dynactin complex. The structural basis for interaction between human EB1 family proteins and their associated proteins has not been defined in detail. EB1 family proteins have a calponin homology (CH) domain at their N terminus and an EB1-like C-terminal motif at their C terminus; the functional importance of these domains has not been determined. To better understand functions of human EB1 family proteins and to reveal functional similarities and differences among these proteins, we performed detailed characterizations of interactions between human EB1 family proteins and their associated proteins. We show that amino acids 1-133 of EB1 and EBF3 and the corresponding region of RP1, which contain a CH domain, are necessary and sufficient for binding microtubules, thus demonstrating for the first time that a CH domain contributes to binding microtubules. EB1 family proteins use overlapping but different regions that contain the EB1-like C-terminal motif to associate with APC and p150glued. Neither APC nor p150glued binding domain is necessary for EB1 or EBF3 to induce microtubule bundling, which requires amino acids 1-181 and 1-185 of EB1 and EBF3, respectively. We also determined that the EB1 family protein-binding regions are amino acids 2781-2820 and 18-111 of APC and p150glued, respectively.

Development of human protein reference database as an initial platform for approaching systems biology in humans.

Human Protein Reference Database (HPRD) is an object database that integrates a wealth of information relevant to the function of human proteins in health and disease. Data pertaining to thousands of protein-protein interactions, posttranslational modifications, enzyme/substrate relationships, disease associations, tissue expression, and subcellular localization were extracted from the literature for a nonredundant set of 2750 human proteins. Almost all the information was obtained manually by biologists who read and interpreted >300,000 published articles during the annotation process. This database, which has an intuitive query interface allowing easy access to all the features of proteins, was built by using open source technologies and will be freely available at http://www.hprd.org to the academic community. This unified bioinformatics platform will be useful in cataloging and mining the large number of proteomic interactions and alterations that will be discovered in the postgenomic era.

Expression of functional neurotransmitter receptors in Xenopus oocytes after injection of human brain membranes.

The Xenopus oocyte is a very powerful tool for studies of the structure and function of membrane proteins, e.g., messenger RNA extracted from the brain and injected into oocytes leads to the synthesis and membrane incorporation of many types of functional receptors and ion channels, and membrane vesicles from Torpedo electroplaques injected into oocytes fuse with the oocyte membrane and cause the appearance of functional Torpedo acetylcholine receptors and Cl(-) channels. This approach was developed further to transplant already assembled neurotransmitter receptors from human brain cells to the plasma membrane of Xenopus oocytes. Membranes isolated from the temporal neocortex of a patient, operated for intractable epilepsy, were injected into oocytes and, within a few hours, the oocyte membrane acquired functional neurotransmitter receptors to gamma-aminobutyric acid, alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid, kainate, and glycine. These receptors were also expressed in the plasma membrane of oocytes injected with mRNA extracted from the temporal neocortex of the same patient. All of this makes the Xenopus oocyte a more useful model than it already is for studies of the structure and function of many human membrane proteins and opens the way to novel pathophysiological investigations of some human brain disorders.

The family of toxin-related ecto-ADP-ribosyltransferases in humans and the mouse.

ADP-ribosyltransferases including toxins secreted by Vibrio cholera, Pseudomonas aerurginosa, and other pathogenic bacteria inactivate the function of human target proteins by attaching ADP-ribose onto a critical amino acid residue. Cross-species polymerase chain reaction (PCR) and database mining identified the orthologs of these ADP-ribosylating toxins in humans and the mouse. The human genome contains four functional toxin-related ADP-ribosyltransferase genes (ARTs) and two related intron-containing pseudogenes; the mouse has six functional orthologs. The human and mouse ART genes map to chromosomal regions with conserved linkage synteny. The individual ART genes reveal highly restricted expression patterns, which are largely conserved in humans and the mouse. We confirmed the predicted extracellular location of the ART proteins by expressing recombinant ARTs in insect cells. Two human and four mouse ARTs contain the active site motif (R-S-EXE) typical of arginine-specific ADP-ribosyltransferases and exhibit the predicted enzyme activities. Two other human ARTs and their murine orthologues deviate in the active site motif and lack detectable enzyme activity. Conceivably, these ARTs may have acquired a new specificity or function. The position-sensitive iterative database search program PSI-BLAST connected the mammalian ARTs with most known bacterial ADP-ribosylating toxins. In contrast, no related open reading frames occur in the four completed genomes of lower eucaryotes (yeast, worm, fly, and mustard weed). Interestingly, these organisms also lack genes for ADP-ribosylhydrolases, the enzymes that reverse protein ADP-ribosylation. This suggests that the two enzyme families that catalyze reversible mono-ADP-ribosylation either were lost from the genomes of these nonchordata eucaryotes or were subject to horizontal gene transfer between kingdoms.

Targeting assay to study the cis functions of human telomeric proteins: evidence for inhibition of telomerase by TRF1 and for activation of telomere degradation by TRF2.

We investigated the control of telomere length by the human telomeric proteins TRF1 and TRF2. To this end, we established telomerase-positive cell lines in which the targeting of these telomeric proteins to specific telomeres could be induced. We demonstrate that their targeting leads to telomere shortening. This indicates that these proteins act in cis to repress telomere elongation. Inhibition of telomerase activity by a modified oligonucleotide did not further increase the pace of telomere erosion caused by TRF1 targeting, suggesting that telomerase itself is the target of TRF1 regulation. In contrast, TRF2 targeting and telomerase inhibition have additive effects. The possibility that TRF2 can activate a telomeric degradation pathway was directly tested in human primary cells that do not express telomerase. In these cells, overexpression of full-length TRF2 leads to an increased rate of telomere shortening.

Regulation of microtubule assembly by human EB1 family proteins.

The EB1 family proteins are highly conserved microtubule-associated proteins. The EB1 protein in yeast has been shown to play an important role in regulating microtubule dynamics and chromosome segregation. Human EB1 family proteins include EB1, RP1 and EBF3. Although EB1 and RP1 have been shown to associate with microtubules, the subcellular localization of endogenous EBF3 had not been characterized. The function of human EB1 family proteins was also not clear. We therefore investigated the cellular localization of EBF3 and the regulation of microtubule organization by EB1 family proteins. As do EB1 and RP1, EBF3 was found to colocalize with microtubules, preferentially at their plus ends, throughout the cell cycle. Moreover, there was a very strong EBF3 signal at the centrosome in interphase cells and at the spindle poles in mitotic cells. When EB1 family proteins were overexpressed, they associated with the entire microtubule cytoskeleton. In addition, EB1 and EBF3 induced microtubule bundling in some cells overexpressing these proteins. These microtubule bundles were more resistant to nocodazole and were more acetylated than regular microtubules. Our results demonstrate for the first time that human EB1 family proteins could regulate microtubule assembly and stability.

A Murine Ortholog of the Human Serpin SCCA2 Maps to Chromosome 1 and Inhibits Chymotrypsin-like Serine Proteinases

Squamous cell carcinoma antigens (SCCA) 1 and 2 are inhibitory members of the high-molecular-weight serine proteinase inhibitor (serpin) family. The biological functions of SCCA1 and 2 are unknown. One approach to determining the function of human proteins is to study orthologs in other species, such as the mouse. The purpose of this study was to determine whether orthologs to human SCCA1 or 2 exist in the mouse. We report the identification and characterization of a novel serpin, sqn5 (now designatedScca2). Comparative amino acid sequence analysis suggests thatScca2is a member of the ov-serpin subfamily of serpins with highest homology to SCCA1 and SCCA2. Fluorescencein situhybridization revealed that theScca2mapped nearBcl2on mouse chromosome 1. This region is syntenic with the human locus for SCCA1 and SCCA2 on 18q21.3. The tissue expression patterns as determined by RT-PCR showed a restricted distribution.Scca2was detected in the lung, thymus, skin, and uterus, as are SCCA1 and SCCA2. Unlike the SCCAs, however,Scca2was detected also in the gastrointestinal tract. Enzyme-inhibition assays using a GST–SCCA2 fusion protein revealed that SCCA2 inhibited chymotrypsin-like serine proteinases, but not papain-like cysteine proteinases. SCCA2 inhibited CTSG at 1:1 stoichiometry and with a second-order rate constant ofkass= 1.7 × 105M−1s−1. SCCA2 also inhibited human mast cell chymase but the stoichiometry was 2:1, and the second-order rate constant waskass= 0.9 × 104M−1s−1. This inhibitory profile is identical to that observed for human SCCA2. Based on these findings,Scca2appears to be the murine ortholog of human SCCA2.

TAF-like functions of human cytomegalovirus immediate-early proteins.

The human cytomegalovirus (HCMV) major immediate-early (IE) proteins IEP86 (IE2(579aa)) and IEP72 (IE1(491aa)) can transcriptionally activate a variety of simple promoters containing a TATA element and one upstream transcription factor binding site. In our previous studies, transcriptional activation was shown to correlate with IEP86 binding to both the TATA-box binding protein (TBP) and the transcription factor bound upstream. IEP72 often synergistically affects the activation by IEP86, although it has not previously been shown to directly interact in vitro with IEP86, TBP, or transcription factors (e.g., Sp1 and Tef-1) bound by IEP86. We report biochemical and genetic evidence suggesting that the major IE proteins may perform a function similar to that of the TBP-associated factors (TAFs) which make up TFIID. Consistent with this model, we found that the major IE proteins interact with a number of TAFs. In vitro, IEP86 bound with drosophila TAF(II)110 (dTAF(II)110) and human TAF(II)130 (hTAF(II)130), while IEP72 bound dTAF(II)40, dTAF(II)110, and hTAF(II)130. Regions on major IE proteins which mediate binding have been defined. In addition, our data indicate that both IEP72 and IEP86 can bind simultaneously to hTAF(II)130, suggesting that this TAF may provide bridging interactions between the two proteins for transcriptional activation and synergy. In agreement, a transcriptional activation mutant of IEP72 is unable to participate in bridging. Confirmation that these in vitro interactions were relevant was provided by data showing that both IEP72 and IEP86 copurify with TFIID and coimmunoprecipitate with purified TFIID derived from infected cell nuclei. To further support a TAF-like function of the IE proteins, we have found that the IE proteins expressed from the intact major IE gene, and to a lesser extent IEP86 alone, can rescue the temperature-sensitive (ts) transcriptional defect in TAF(II)250 in the BHK-21 cell line ts13. Analyses of mutations in the major IE region show that IEP86 is essential for rescue and that IEP72 augments its effect, and that mutations which affect TAF interactions are debilitated in rescue. Our data, showing that the IE proteins can bind with TFIID and rescue a ts transcriptional defect in TAF(II)250, support the model that the IE proteins perform a TAF-like function as components of TFIID.

Functions of human papillomavirus proteins.

Cervical cancer is the second leading cause of deaths from cancer among women worldwide with approximately 500 000 deaths annually. Epidemiologic studies have implicated a sexually transmitted agent as a cause of cervical cancer, and molecular virology studies over the past 10 years have established a strong association between specific human papillomavirus (HPV) types and certain anogenital carcinomas, including cervical cancer (reviewed in zur Hausen and Schneider 1987). Over 65 different HPV types have now been described, and each is associated with a specific clinical entity (DeVilliers 1989). Approximately 20 or 25 HPVs have been associated with anogenital lesions; these HPVs have been further classified as either “low-risk” or “high-risk” types based on the preneoplastic character of the clinical lesions with which they are associated. Low-risk HPVs such as HPV-6 and HPV-11 are generally associated with venereal warts or condyloma acuminata which only rarely progress to malignancy. The high-risk HPVs include HPV-16 and HPV-18 and these are associated with squamous intraepithelial neoplasias which are potentially precancerous. In the cervix, they are associated with cervical intraepithelial neoplasia, or CIN. These CIN lesions are considered preneoplastic in that a small percentage of high-grade CIN lesions will progress to cervical cancer. Approximately 70% of human cervical cancers contain either HPV-16 or HPV-18 DNA (zur Hausen and Schneider 1987). Indeed, HPV-16 and HPV-18 DNA were originally isolated from human cervical carcinoma tissues (Durst et al. 1983; Boshart et al. 1984). Other high-risk HPVs, including types 31, 33, 35, 39, 45, 51, and 52, have subsequently been identified and have also been associated with CIN lesions and with invasive cervical carcinomas. All together, approximately 85% of cervical cancers can be shown to contain DNA of one of the high-risk HPV types (Riou et al. 1990).

Biochemistry and physiological function of human milk proteins

Human milk has many unique properties that benefit the breast-fed infant. Several of these properties reside in the protein fraction of human milk; eg, host defense factors (such as immunoglobulins, lysozyme, and lactoferrin), digestive enzymes (lipases, proteases, amylase), specific binding proteins, and growth factors. Increased knowledge of human milk proteins and their biochemistry will aid our understanding of their physiological significance in the infant.

Chemistry and function of human plasma proteins.

AbstractHuman blood plasma contains a large number of proteins. New analytical and preparative techniques have so far permitted the isolation of more than one hundred such proteins; about ninety percent of these were first characterized in the last 30 years. The plasma proteins include components of the clotting and complement systems as well as proteinase inhibitors, immunoglobulins, lipoproteins, and carrier proteins. The biological function of some of the plasma proteins is not yet known. Deficiency of one or more plasma proteins usually causes serious health disorders, the best known example being hemophilia. Several biologically active proteins can be gained from blood plasma; these proteins—for example the blood clotting factors—are of great prophylactic and therapeutic importance and allow a better exploitation of the valuable plasma than can be obtained by means of transfusion.