Starch-binding domains as CBM families–history,occurrence, structure,function and evolution

The term “starch-binding domain” (SBD) has been applied to a domain within an amylolytic enzyme that gave the enzyme the ability to bind onto raw, i.e. thermally untreated, granular starch. An SBD is a special case of a carbohydrate-binding domain, which in general, is a structurally and functionally independent protein module exhibiting no enzymatic activity but possessing potential to target the catalytic domain to the carbohydrate substrate to accommodate it and process it at the active site. As so-called families, SBDs together with other carbohydrate-binding modules (CBMs) have become an integral part of the CAZy database (http://www.cazy.org/). The first two well-described SBDs, i.e. the C-terminal Aspergillus-type and the N-terminal Rhizopus-type have been assigned the families CBM20 and CBM21, respectively. Currently, among the 85 established CBM families in CAZy, fifteen can be considered as families having SBD functional characteristics: CBM20, 21, 25, 26, 34, 41, 45, 48, 53, 58, 68, 69, 74, 82 and 83. All known SBDs, with the exception of the extra long CBM74, were recognized as a module consisting of approximately 100 residues, adopting a β-sandwich fold and possessing at least one carbohydrate-binding site. The present review aims to deliver and describe: (i) the SBD identification in different amylolytic and related enzymes (e.g., CAZy GH families) as well as in other relevant enzymes and proteins (e.g., laforin, the β-subunit of AMPK, and others); (ii) information on the position in the polypeptide chain and the number of SBD copies and their CBM family affiliation (if appropriate); (iii) structure/function studies of SBDs with a special focus on solved tertiary structures, in particular, as complexes with α-glucan ligands; and (iv) the evolutionary relationships of SBDs in a tree common to all SBD CBM families (except for the extra long CBM74). Finally, some special cases and novel potential SBDs are also introduced.     

Checklist of the families Scathophagidae,Fanniidae and?Muscidae of Finland (Insecta,Diptera)

A revised checklist of the Scathophagidae, Fanniidae and Muscidae recorded from Finland is presented. Phaonia amicula Villeneuve, 1922 is noted from Finland for the first time.     

Checklist of the families Anisopodidae,Bibionidae, Canthyloscelididae,Mycetobiidae, Pachyneuridae and?Scatopsidae (Diptera) of Finland

A checklist of the families Anisopodidae, Bibionidae, Canthyloscelididae, Mycetobiidae, Pachyneuridae and Scatopsidae (Diptera) recorded from Finland. The Finnish species of these families were last listed in 1980. After that two species of Anisopodidae, four species of Bibionidae and six species of Scatopsidae have been added to the Finnish fauna and two species of Scatopsidae have been removed from the Finnish fauna.     

Checklist of the families Lonchopteridae and Phoridae?of Finland (Insecta,Diptera)

A checklist of the Lonchopteridae and Phoridae recorded from Finland is presented.     

Review of Colombian Conchostraca (Crustacea) — ecological aspects and life cycles — families Lynceidae,Limnadiidae, Leptestheriidae and Metalimnadiidae

This study gives an overview of our current knowledge of the ecology and distribution patterns of Colombian conchostracans. Colombian euphyllopods are generally restricted to the warm tropical lowlands. OnlyCyclestheria hislopi can be found year-round in larger semipermanent waters and living sympatrically with abundant predators, such as planktivorous fish. The other conchostracans are restricted to the typical habitat of temporary waters.Eulimnadia magadalenensis is especially adapted to very short-term temporary ponds in relatively arid zones andE. colombiensis prefers somewhat cooler ponds of a longer duration. The two species can be found sympatrically in intermediate climatic conditions. A third form,Eulimnadia cf. geayi cohabits with the two other species in the lower Magdalena Valley, its ecological role is not clear.Limnadia orinoquiensis is the selvatic substitute of the open savannah conchostracan fauna (mainlyEulimnadia forms) living in pools in forest clearings in the vicinity of the Upper Orinoco.Four species of Lynceidae were found, twoLynceus and twoParalimnetis. Their distribution patterns are not yet clear, they prefer smaller temporary ponds of moderated temperatures. Two undescribed species ofLeptestheria were found, one restricted to the banks of the Orinoco and the other to one locality in the upper Magdalena Valley, living in ponds with a muddy bottom.Metalimnadia serratura was found in special rock pools of the Guiana Shield in the vicinity of the Orinoco, cohabiting with several other conchostracan species, with differential adaptations to very high water temperatures.     

The γ-crystallin gene families: Sequence and evolutionary patterns

Summary The -crystallin proteins consist of two topologically equivalent domains, each built up out of two similar motifs. They are encoded by a gene family, which already contained five members before the divergence of rodents and primates. A further gene duplication took place in each lineage. To analyze the pattern of evolution within this gene family, the coding sequences of six human genes, six rat genes, and four mouse genes were compared. Between species, a uniform rate of evolution of all regions of the protein is seen. The ratio of synonymous to nonsynonymous substitution in the human/rat or human/mouse comparison is much lower than the ratio when rat and mouse are compared indicating that the -crystallin proteins are better conserved in the rodent lineage. Within species, the regions encoding the two external motifs I and III of the protein show a greater extent of nonsynonymous substitution than the regions encoding the two internal protein motifs II and IV. The low extent of synonymous substitution between the second exons (encoding motifs I and II) of the rat -crystallin genes suggests the frequent occurrence of gene conversion. In contrast, a high extent of synonymous substitution is found in exon 3 (encoding motifs III and IV) of the rat genes. The same phenomenon is seen within the human gene family. The frequencies of occurrence of the various dinucleotides deviate less from those predicted from the frequencies of occurrence of each individual nucleotide in the second exons than in the third exons. The sequences of the third exons are significantly depleted in CpG, ApA, and GpT and enriched in CpT and GpA.     

The incidence of ΔF508 CF mutation,and associated haplotypes,in a sample of English CF families

Summary Data are presented for ΔF508 screening and KM19/XV2c haplotype analysis of 195 cystic fibrosis (CF) chromosomes from the British Caucasian population. We report the frequency of ΔF508 in this group to be 80% and find pronounced disequilibrium between the deletion and the KM 2, XV 1 haplotype. Haplotype analysis of 71 normal chromosomes is also presented. We report one individual who had meconium ileus and who does not have the ΔF508 mutation on either chromosome.     

Checklist of the smaller families of Opomyzoidea,Anthomyzidae, Asteiidae,Aulacigastridae, Clusiidae,Odiniidae, Opomyzidae and Periscelididae (Diptera)?of?Finland

A species checklist is presented for Finland covering seven smaller families of Opomyzoidea: Anthomyzidae, Asteiidae, Aulacigastridae, Clusiidae, Odiniidae, Opomyzidae and Periscelididae (Diptera).     

Nonvesicular sterol transport: two protein families and a sterol sensor?

Sterols, essential components of eukaryotic membranes, are actively transported between cellular membranes. Although it is known that both vesicular and non-vesicular means are used to move sterols, the molecules and molecular mechanisms involved have yet to be identified. Recent studies point to a key role for oxysterol binding protein (OSBP) and its related proteins (ORPs) in nonvesicular sterol transport. Here, evidence that OSBP and ORPs are bona fide sterol carriers is discussed. In addition, I hypothesize that ATPases associated with various cellular activities regulate the recycling of soluble lipid carriers and that the Niemann Pick C1 protein facilitates the delivery of sterols from endosomal membranes to ORPs and/or the ensuing membrane dissociation of ORPs.     

Functional redundancy and compensation among members of gap junction protein families?

Gap junctions are intercellular conduits for small molecules made up by protein subunits called connexins. A large number of connexin genes were found in mouse and man, and most cell types express several connexins, lending support to the view that redundancy and compensation among family members exist. This review gives an overview of the current knowledge on redundancy and functional compensation - or lack thereof. It takes into account the different properties of connexin subunits which comprise gap junctional intercellular channels, but also the compatibility of connexins in gap junctions. Most insight has been gained by the investigation of mice deficient for one or more connexins and transgenic mice with functional replacement of one connexin gene by another. Most single deficient mice show phenotypical alterations limited to critical developmental time points or to specific organs and tissues, while mice doubly deficient for connexins expressed in the same cell type usually show more severe phenotypical alterations. Replacement of a connexin by another connexin in some cases gave rise to rescue of phenotypical alterations of connexin deficiencies, which were restricted to specific tissues. In many tissues, connexin substitution did not restore phenotypical alterations of connexin deficiencies, indicating that connexins are specialized in function. In some cases, fatal consequences arose from the replacement. The current consensus gained from such studies is that redundancy and compensation among connexins exists at least to a limited extent. This article is part of a Special Issue entitled: The Communicating junctions, composition, structure and characteristics.     

5′ and 3′ SINE-PCR allows genotyping of pig families without cloning and sequencing steps

A microsatellite-containing clone, isolated from a pig Chromosome (Chr) 1-specific library was characterized by sequencing and computer analysis. The (CA)₁₇ microsatellite motif was located at the 3 end of a short interspersed element (SINE) sequence at the position normally occupied by the oligo (A) stretch. Further computer analysis indicated that 12% of published pig SINE sequences contain dinucleotide repeat motifs adjacent to their 3 ends. By performing PCR with a single SINE primer in combination with a panel of arbitrarily selected unique primers, we have demonstrated that, as in human, polymorphisms can be detected and typed in pig family DNAs. A large number of SINE primer x unique primer combinations have been screened for the ability to detect polymorphisms in pig reference family DNAs. This approach does not require prior sequence information other than that of the pig SINE. We have also found polymorphisms at the 5 ends of pig SINE sequences by similar methods, but with a primer facing out to the 5 end of the SINE.     

The sterol-sensing domain: multiple families, a unique role?

The "sterol-sensing domain" (SSD) is conserved across phyla and is present in several membrane proteins, such as Patched (a Hedgehog receptor) and NPC-1 (the protein defective in Niemann-Pick type C1 disease). The role of the SSD is perhaps best understood from the standpoint of its involvement in cholesterol homeostasis. This article discusses how the SSD appears to function as a regulatory domain involved in linking vesicle trafficking and protein localization with such varied processes as cholesterol homeostasis, cell signalling and cytokinesis.     

4,6-α-glucanotransferase, a novel enzyme that structurally and functionally provides an evolutionary link between glycoside hydrolase enzyme families 13 and 70

Lactobacillus reuteri 121 uses the glucosyltransferase A (GTFA) enzyme to convert sucrose into large amounts of the α-d-glucan reuteran, an exopolysaccharide. Upstream of gtfA lies another putative glucansucrase gene, designated gtfB. Previously, we have shown that the purified recombinant GTFB protein/enzyme is inactive with sucrose. Various homologs of gtfB are present in other Lactobacillus strains, including the L. reuteri type strain, DSM 20016, the genome sequence of which is available. Here we report that GTFB is a novel α-glucanotransferase enzyme with disproportionating (cleaving α1→4 and synthesizing α1→6 and α1→4 glycosidic linkages) and α1→6 polymerizing types of activity on maltotetraose and larger maltooligosaccharide substrates (in short, it is a 4,6-α-glucanotransferase). Characterization of the types of compounds synthesized from maltoheptaose by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS), methylation analysis, and 1-dimensional ¹H nuclear magnetic resonance (NMR) spectroscopy revealed that only linear products were made and that with increasing degrees of polymerization (DP), more α1→6 glycosidic linkages were introduced into the final products, ranging from 18% in the incubation mixture to 33% in an enriched fraction. In view of its primary structure, GTFB clearly is a member of the glycoside hydrolase 70 (GH70) family, comprising enzymes with a permuted (β/α)₈ barrel that use sucrose to synthesize α-d-glucan polymers. The GTFB enzyme reaction and product specificities, however, are novel for the GH70 family, resembling those of the GH13 α-amylase type of enzymes in using maltooligosaccharides as substrates but differing in introducing a series of α1→6 glycosidic linkages into linear oligosaccharide products. We conclude that GTFB represents a novel evolutionary intermediate between the GH13 and GH70 enzyme families, and we speculate about its origin.     

Polymorphic DNA haplotypes and ΔF508 deletion in 212 Italian CF families

Summary Haplotype data based on the DNA markers closely linked to the cystic fibrosis (CF) gene have been used to correlate the presence of the 3 by specific deletion (ΔF508) in 424 CF chromosomes from 212 Italian CF families. The distribution and the frequency of the F508 deletion on CF chromosomes in our sample suggests the presence of at least a second mutation in the same ancestral haplotype.     

Fungal α-arabinofuranosidases of glycosyl hydrolase families 51 and 54 show a dual arabinofuranosyl- and galactofuranosyl-hydrolyzing activity

Abstract Aspergillus niger possesses a galactofuranosidase activity, however, the corresponding enzyme or gene encoding this enzyme has never been identified. As evidence is mounting that enzymes exist with affinity for both arabinofuranose and galactofuranose, we investigated the possibility that α-l-arabinofuranosidases, encoded by the abfA and abfB genes, are responsible for the galactofuranosidase activity of A. niger. Characterization of the recombinant AbfA and AbfB proteins revealed that both enzymes do not only hydrolyze p-nitrophenyl-α-l-arabinofuranoside (pNp-α-Araf) but are also capable of hydrolyzing p-nitrophenyl-β-d-galactofuranoside (pNp-β-Galf). Molecular modeling of the AbfB protein with pNp-β-Galf confirmed the possibility for AbfB to interact with this substrate, similarly as with pNp-α-Araf. We also show that galactomannan, a cell wall compound of A. niger, containing β-linked terminal and internal galactofuranosyl moieties, can be degraded by an enzyme activity that is present in the supernatant of inulin-grown A. niger. Interestingly, purified AbfA and AbfB did not show this hydrolyzing activity toward A. nigergalactomannan. In summary, our studies demonstrate that AbfA and AbfB, α-l-arabinofuranosidases from different families, both contain a galactofuranose (Galf)-hydrolyzing activity. In addition, our data support the presence of a Galf-hydrolase activity expressed by A. niger that is capable of degrading fungal galactomannan.     

Frequency of ΔF508 and haplotype association in Austrian cystic fibrosis families

Summary The frequency of the major mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) gene was analyzed for 113 Austrian cystic fibrosis (CF) patients. An overall frequency of 55% for F508 was found with values of 72% and 13% for patients with pancreatic insufficiency (CF-PI) and those with pancreatic sufficiency (CF-PS), respectively. Furthermore, the distribution of the alleles of the closely linked DNA markers XV2c/KM19/MP6d-9 in our families is described.     

Consistent isomiR expression patterns and 3′ addition events in miRNA gene clusters and families implicate functional and evolutionary relationships

3′ addition events in miRNAs are widely detected and may contribute to miRNA stability, but little is known about details of the events in miRNA gene clusters and families. Here, we performed a comprehensive analysis of isomiR expression patterns and 3′ additions in miRNA gene clusters and families by analyzing high-throughput sequencing dataset. According to dominant modified isomiRs, miRNA members in many miRNA gene clusters and families showed the same 3′ additional non-template nucleotides. Although clustered miRNAs and homologous miRNAs had consistent or inconsistent expression levels, we found many of them showed consistent expression patterns at isomiR levels. These findings revealed similar processing mechanism and 3′ modification event of miRNAs in gene clusters and families through miRNA maturation process. The consistent maturation mechanism may contribute to co-regulate biological processes, and may originate from ancestral miRNA genes through complex duplication history.