The heat shock genes: A family of highly conserved genes with a superbly complex expression pattern

The heat shock genes (hsp genes) are a family of truly ubiquitous genes which have been highly conserved throughout evolution. The protein products of these genes, the heat shock proteins (hsps) are thought to play a protective role in cells (although this may not be their only function). The genes and their products have been the subjects of intense research both at the cellular and molecular levels over the past few years. This review deals with the conservation of the heat shock response and with the expression of the hsp genes under different conditions: they are usually activated as a group by different forms of stress, but can be expressed individually or in subsets at different stages during normal development and the expression of one of them is evoked by the products of different transforming genes. Experimental approaches which have provided information or which have led to hypotheses regarding the molecular details of the mechanisms regulating the expression of the genes are discussed.     

A family of highly conserved glycosomal 2-hydroxyacid dehydrogenases from Phytomonas sp

Phytomonas sp. contains two malate dehydrogenase isoforms, a mitochondrial isoenzyme with a high specificity for oxaloacetate and a glycosomal isozyme that acts on a broad range of substrates (Uttaro, A. D., and Opperdoes, F.R. (1997) Mol. Biochem. Parasitol. 89, 51-59). Here, we show that the low specificity of the latter isoenzyme is the result of a number of recent gene duplications that gave rise to a family of glycosomal 2-hydroxyacid dehydrogenase genes. Two of these genes were cloned, sequenced, and overexpressed in Escherichia coli. Although both gene products have 322 amino acids, share 90.4% identical residues, and have a similar hydrophobicity profile and net charge, their kinetic properties were strikingly different. One isoform behaved as a real malate dehydrogenase with a high specificity for oxaloacetate, whereas the other showed no activity with oxaloacetate but was able to reduce other oxoacids, such as phenyl pyruvate, 2-oxoisocaproate, 2-oxovalerate, 2-oxobutyrate, 2-oxo-4-methiolbutyrate, and pyruvate.     

A novel family of phosphatidylinositol 4-kinases conserved from yeast to humans

Phosphatidylinositolpolyphosphates (PIPs) are centrally involved in many biological processes, ranging from cell growth and organization of the actin cytoskeleton to endo- and exocytosis. Phosphorylation of phosphatidylinositol at the D-4 position, an essential step in the biosynthesis of PIPs, appears to be catalyzed by two biochemically distinct enzymes. However, only one of these two enzymes has been molecularly characterized. We now describe a novel class of phosphatidylinositol 4-kinases that probably corresponds to the missing element in phosphatidylinositol metabolism. These kinases are highly conserved evolutionarily, but unrelated to previously characterized phosphatidylinositol kinases, and thus represent the founding members of a new family. The novel phosphatidylinositol 4-kinases, which are widely expressed in cells, only phosphorylate phosphatidylinositol, are potently inhibited by adenosine, but are insensitive to wortmannin or phenylarsine oxide. Although they lack an obvious transmembrane domain, they are strongly attached to membranes by palmitoylation. Our data suggest that independent pathways for phosphatidylinositol 4-phosphate synthesis emerged during evolution, possibly to allow tight temporal and spatial control over the production of this key signaling molecule.     

Characterization of JDP genes, an evolutionarily conserved J domain-only protein family, from human and moths

We characterized evolutionarily conserved J domain containing protein (JDP) genes from human, Bombyx mori, and Manduca sexta. Each of the JDP proteins contains a J domain at its N-terminus and a highly conserved C-terminal domain. Southern blot analysis revealed that the human JDP1 gene is present as a single copy in the human genome. Expression was higher in brain, heart, and testis than in kidney or stomach. Human JDP1 was mapped in silico to chromosome 10q21.1, which exhibits a conserved synteny with the central region of mouse chromosome 10. Drosophila jdp is located at 99F4-99F11 on the right arm of the third chromosome.     

A highly conserved family of inactivated archaeal B family DNA polymerases

   

A widespread and highly conserved family of apparently inactivated derivatives of archaeal B-family DNA polymerases is described. Phylogenetic analysis shows that the inactivated forms comprise a distinct clade among archaeal B-family polymerases and that, within this clade, Euryarchaea and Crenarchaea are clearly separated from each other and from a small group of bacterial homologs. These findings are compatible with an ancient duplication of the DNA polymerase gene followed by inactivation and parallel loss in some of the lineages although contribution of horizontal gene transfer cannot be ruled out. The inactivated derivative of the archaeal DNA polymerase could form a complex with the active paralog and play a structural role in DNA replication.     

Identification,chromosomal mapping and conserved synteny of porcine Argonaute family of genes

The Argonaute proteins are recently identified and evolutionarily conserved family with two subfamilies Ago and Piwi, which play important roles in small RNA pathways. Most species have eight Argonaute members in their genomes, ranging from 1 to 27. Here we report identification of six Argonaute genes in pig, four members of the Ago subfamily (Ago1, Ago2, Ago3 and Ago4) and two members of the Piwi subfamily (Piwil1 and Piwil2), which were predicted to encode proteins of 857, 860, 860, 861, 861 and 985 amino acids, respectively. Phylogenetic analysis showed that the porcine Ago and Piwi genes were clustered into relevant branch of mammalian Argonaute members. The porcine Ago4- Ago1-Ago3 genes are linked together at the p12 of the chromosome 6, while Ago2 is located at the p15 of the chromosome 4. The porcine Piwil1 and Piwil2 are mapped together onto the chromosome 14, at the q14 and q11 respectively. Comparatively mapping of the Argonaute members on chromosomes showed that linkage group of the Ago4-Ago1-Ago3 and several neighborhood genes is evolutionarily conserved from chicken to mammals. The genes Piwil1 and Piwil2 are separated onto different chromosomes from fish to mammals, with exception to this tendency in both pig and stickleback, indicating an opposite tendency of recombination together or non-disjunction of these two genes during speciation. Further expression analysis showed an ubiquitous expression pattern of Ago members, oppositely a restricted expression pattern in gonads of the Piwi members, suggesting distinct potential roles of the porcine Argonaute genes.     

A conserved family of cellular genes related to the baculovirus iap gene and encoding apoptosis inhibitors.

The baculovirus inhibitor of apoptosis gene, iap, can impede cell death in insect cells. Here we show that iap can also prevent cell death in mammalian cells. The ability of iap to regulate programmed cell death in widely divergent species raised the possibility that cellular homologs of iap might exist. Consistent with this hypothesis, we have isolated Drosophila and human genes which encode IAP-like proteins (dILP and hILP). Like IAP, both dILP and hILP contain amino-terminal baculovirus IAP repeats (BIRs) and carboxy-terminal RING finger domains. Human ilp encodes a widely expressed cytoplasmic protein that can suppress apoptosis in transfected cells. An analysis of the expressed sequence tag database suggests that hilp is one of several human genes related to iap. Together these data suggest that iap and related cellular genes play an evolutionarily conserved role in the regulation of apoptosis.     

A small family of nodule specific genes from soybean.

The primary structure of two nodule specific soybean genes are presented. The two genes code for primary products of 20.0 (nodulin 20) and 22.7 (nodulin 22) kdaltons, respectively. Both genes are related to the nodulin 23 and 44 genes. Alignment of the deduced amino acid sequences of all four genes revealed three domains of high homology interrupted by highly diverged regions due to numerous duplication and insertion events. The first conserved domain codes for a putative signal peptide, while the two others each contain four Cys residues that can be arranged in a way reminiscent of the metal binding domains present in some enzymes and in several DNA binding proteins.     

A review on mesopelagic fishes belonging to family Myctophidae

Myctophids are mesopelagic fishes belonging to family Myctophidae. They are represented by approx. 250 species in 33 genera. Called as “Lanternfishes”, they inhabit all oceans except the Arctic. They are well-known for exhibiting adaptations to oxygen minimum zones (OMZ-in the upper 2,000 m) and also performing diel vertical migration between the meso- and epipelagic regions. True to their name, lanternfishes possess glowing effect due to the presence of the photophores systematically arranged on their body, one of the important characteristic adding to their unique ecological features. Mid-water trawling is a conventional method of catching these fishes which usually accounts for biomass approx. in million tones as seen in Arabian Sea (20–100 million) or Southern ocean (70–200 million). Ecologically, myctophids link primary consumers like copepods, euphausiids and top predators like squids, whales and penguins in a typical food web. Lantern fishes become a major part of deep scattering layers (DSL) during migration along with other fauna such as euphausiids, medusae, fish juveniles, etc. Like any other marine organisms, Myctophids are susceptible to parasites like siphonostomatoid copepods, nematode larvae etc. in natural habitats. They are important contributors of organic carbon in the form of their remnants and fast sinking faeces, which get deposited on ocean beds. Economically, they are a good source of protein, lipids and minerals, which is used as fishmeal for poultry and animal feed and as crop fertilizers. Few species are considered edible, but proper processing difficulties on a higher scale limit myctophids as human food. Myctophids have a life span of approx. 1–5 years and low fecundity rates (100–2,000 eggs per spawn). This trait is a disadvantage, if continuous utilization of their population, for e.g., for fish meal industries etc., occurs without giving them a chance to revive and recover. Hence, research in this area also should be given utmost importance. In this paper, we have tried to compile information and ideas from various sources of myctophid research around the world, particularly from the Indian Ocean, to understand their ecological and economic importance and also to put forth new ideas to bring about conservation and restoration of this vulnerable resource.     

Intracisternal A-particle genes in Mus musculus: a conserved family of retrovirus-like elements.

The structural organization of intracisternal A-particle genes has been studied, using isolates from a mouse gene library in lambda phage Charon 4A. The predominant gene form among the isolates was 7.3 kilobases (kb) in length. R-loops between the 7-kb (35S) A-particle genomic ribonucleic acid and several of these genes were colinear, with no visible evidence of intervening deoxyribonucleic acid sequences. One recombinant was found with an A-particle gene that contained a 1.7-kb deletion. Using the deletion as a reference, the deoxyribonucleic acid and ribonucleic acid homology regions were localized with respect to one another and to the restriction map: the 5' terminus of the ribonucleic acid was several hundred base pairs within the 5' end of the deoxyribonucleic acid homology region. Restriction endonuclease fragments encompassing the 5' and 3' regions of one 7.3-kb gene were separately subcloned into pBR322. Heteroduplexes between the two subclones revealed an approximately 300-base pair segment of terminally redundant sequences. The cloned 3' fragment hybridized with restriction fragments from the 5' end of several other A-particle genes, demonstrating the presence of common (though not necessarily identical) terminally repeated sequences. A-particle genes varied in the occurrence of specific restriction sites at characteristic internal loci. However, heteroduplexes between several variant 7.3-kb genes showed continuous homology regions even when spread under stringent hybridization conditions. The relative abundance of restriction site variants was highly conserved in 12 laboratory strains of Mus musculus, in embryonic and adult tissues of a single inbred strain, and in the SC-1 cell line of feral mouse origin, but appeared to differ in a feral Japanese substrain, Mus musculus molossinus. Some evidence suggests that subsets of A-particle genes may have similar flanking sequences. The results are discussed in terms of the evolution of this multigene family.     

A family of human microRNA genes from miniature inverted-repeat transposable elements

While hundreds of novel microRNA (miRNA) genes have been discovered in the last few years alone, the origin and evolution of these non-coding regulatory sequences remain largely obscure. In this report, we demonstrate that members of a recently discovered family of human miRNA genes, hsa-mir-548, are derived from Made1 transposable elements. Made1 elements are short miniature inverted-repeat transposable elements (MITEs), which consist of two 37 base pair (bp) terminal inverted repeats that flank 6 bp of internal sequence. Thus, Made1 elements are nearly perfect palindromes, and when expressed as RNA they form highly stable hairpin loops. Apparently, these Made1-related structures are recognized by the RNA interference enzymatic machinery and processed to form 22 bp mature miRNA sequences. Consistent with their origin from MITEs, hsa-mir-548 genes are primate-specific and have many potential paralogs in the human genome. There are more than 3,500 putative hsa-mir-548 target genes; analysis of their expression profiles and functional affinities suggests cancer-related regulatory roles for hsa-mir-548. Taken together, the characteristics of Made1 elements, and MITEs in general, point to a specific mechanism for the generation of numerous small regulatory RNAs and target sites throughout the genome. The evolutionary lineage-specific nature of MITEs could also provide for the generation of novel regulatory phenotypes related to species diversification. Finally, we propose that MITEs may represent an evolutionary link between siRNAs and miRNAs.     

Epigenetic regulation of genes during development： A conserved theme from flies to mammals

Eukaryotic genome is organized in form of chromatin within the nucleus. This organization is important for compaction of DNA as well as for the proper expression of the genes. During early embryonic development, genomic packaging receives variety of signals to eventually set up cell type specific expression patterns of genes. This process of regulated chromatinization leads to "cell type specific epigenomes". The expression states attained during differentiation process need to be maintained subsequently throughout the life of the organism. Epigenetie modifications are responsible for chromatin dependent regulatory mechanism and play a key role in maintenance of the expression state-a process referred to as cellular memory. Another key feature in the packaging of the genome is formation of chro- matin domains that are thought to be structural as well as functional units of the higher order chromatin organization. Boundary elements that function to define such domains set the limits of regulatory elements and that of epigenetie modifications. This connection of epige- netic modification, chromatin structure and genome organization has emerged from several studies. Hox genes are among the best studied in this context and have led to the significant understanding of the epigenetic regulation during development. Here we discuss the evolu- tionarily conserved features of epigenetic mechanisms emerged from studies on homeotic gene clusters.     

A conserved catalytic residue in the ubiquitin-conjugating enzyme family

Ubiquitin (Ub) regulates diverse functions in eukaryotes through its attachment to other proteins. The defining step in this protein modification pathway is the attack of a substrate lysine residue on Ub bound through its C-terminus to the active site cysteine residue of a Ub-conjugating enzyme (E2) or certain Ub ligases (E3s). So far, these E2 and E3 cysteine residues are the only enzyme groups known to participate in the catalysis of conjugation. Here we show that a strictly conserved E2 asparagine residue is critical for catalysis of E2- and E2/RING E3-dependent isopeptide bond formation, but dispensable for upstream and downstream reactions of Ub thiol ester formation. In contrast, the strictly conserved histidine and proline residues immediately upstream of the asparagine are dispensable for catalysis of isopeptide bond formation. We propose that the conserved asparagine side chain stabilizes the oxyanion intermediate formed during lysine attack. The E2 asparagine is the first non-covalent catalytic group to be proposed in any Ub conjugation factor.